diff --git a/cartographer/CMakeLists.txt b/cartographer/CMakeLists.txt
index c149ccf..92f4d9d 100644
--- a/cartographer/CMakeLists.txt
+++ b/cartographer/CMakeLists.txt
@@ -18,6 +18,5 @@ add_subdirectory("kalman_filter")
 add_subdirectory("mapping")
 add_subdirectory("mapping_2d")
 add_subdirectory("mapping_3d")
-add_subdirectory("proto")
 add_subdirectory("sensor")
 add_subdirectory("transform")
diff --git a/cartographer/mapping/CMakeLists.txt b/cartographer/mapping/CMakeLists.txt
index a05d067..089f9bf 100644
--- a/cartographer/mapping/CMakeLists.txt
+++ b/cartographer/mapping/CMakeLists.txt
@@ -140,7 +140,7 @@ google_library(mapping_submaps
     common_port
     mapping_2d_probability_grid
     mapping_probability_values
-    mapping_proto_submaps
+    mapping_proto_submap_visualization
     mapping_trajectory_node
     transform_transform
 )
@@ -179,7 +179,7 @@ google_library(mapping_trajectory_node
     trajectory_node.h
   DEPENDS
     common_time
-    proto_trajectory
+    mapping_proto_trajectory
     sensor_laser
     transform_rigid_transform
     transform_transform
diff --git a/cartographer/mapping/proto/CMakeLists.txt b/cartographer/mapping/proto/CMakeLists.txt
index 77da2d0..aa538a9 100644
--- a/cartographer/mapping/proto/CMakeLists.txt
+++ b/cartographer/mapping/proto/CMakeLists.txt
@@ -30,7 +30,7 @@ google_proto_library(mapping_proto_sparse_pose_graph
   SRCS
     sparse_pose_graph.proto
   DEPENDS
-    proto_trajectory
+    mapping_proto_trajectory
     transform_proto_transform
 )
 
@@ -42,9 +42,16 @@ google_proto_library(mapping_proto_sparse_pose_graph_options
     mapping_sparse_pose_graph_proto_optimization_problem_options
 )
 
-google_proto_library(mapping_proto_submaps
+google_proto_library(mapping_proto_submap_visualization
   SRCS
-    submaps.proto
+    submap_visualization.proto
+  DEPENDS
+    transform_proto_transform
+)
+
+google_proto_library(mapping_proto_trajectory
+  SRCS
+    trajectory.proto
   DEPENDS
     transform_proto_transform
 )
diff --git a/cartographer/mapping/proto/sparse_pose_graph.proto b/cartographer/mapping/proto/sparse_pose_graph.proto
index e646b8b..13ce381 100644
--- a/cartographer/mapping/proto/sparse_pose_graph.proto
+++ b/cartographer/mapping/proto/sparse_pose_graph.proto
@@ -16,8 +16,8 @@ syntax = "proto2";
 
 package cartographer.mapping.proto;
 
+import "cartographer/mapping/proto/trajectory.proto";
 import "cartographer/transform/proto/transform.proto";
-import "cartographer/proto/trajectory.proto";
 
 message SparsePoseGraph {
   message Constraint {
@@ -50,5 +50,5 @@ message SparsePoseGraph {
   }
 
   repeated Constraint constraint = 2;
-  repeated .cartographer.proto.Trajectory trajectory = 4;
+  repeated Trajectory trajectory = 4;
 }
diff --git a/cartographer/mapping/proto/submaps.proto b/cartographer/mapping/proto/submap_visualization.proto
similarity index 100%
rename from cartographer/mapping/proto/submaps.proto
rename to cartographer/mapping/proto/submap_visualization.proto
diff --git a/cartographer/proto/trajectory.proto b/cartographer/mapping/proto/trajectory.proto
similarity index 96%
rename from cartographer/proto/trajectory.proto
rename to cartographer/mapping/proto/trajectory.proto
index 11fe086..63858c8 100644
--- a/cartographer/proto/trajectory.proto
+++ b/cartographer/mapping/proto/trajectory.proto
@@ -14,9 +14,9 @@
 
 syntax = "proto2";
 
-import "cartographer/transform/proto/transform.proto";
+package cartographer.mapping.proto;
 
-package cartographer.proto;
+import "cartographer/transform/proto/transform.proto";
 
 option java_outer_classname = "TrajectoryOuterClass";
 
diff --git a/cartographer/mapping/sparse_pose_graph.cc b/cartographer/mapping/sparse_pose_graph.cc
index e9534d8..ea3b021 100644
--- a/cartographer/mapping/sparse_pose_graph.cc
+++ b/cartographer/mapping/sparse_pose_graph.cc
@@ -121,7 +121,7 @@ proto::SparsePoseGraph SparsePoseGraph::ToProto() {
   }
 
   // TODO(whess): Support multi-trajectory.
-  ::cartographer::proto::Trajectory* const trajectory = proto.add_trajectory();
+  proto::Trajectory* const trajectory = proto.add_trajectory();
   *trajectory = mapping::ToProto(GetTrajectoryNodes());
   const std::vector<std::vector<const Submaps*>> components =
       GetConnectedTrajectories();
diff --git a/cartographer/mapping/submaps.h b/cartographer/mapping/submaps.h
index 9ac4307..faa6bfc 100644
--- a/cartographer/mapping/submaps.h
+++ b/cartographer/mapping/submaps.h
@@ -36,7 +36,7 @@
 #include "cartographer/common/math.h"
 #include "cartographer/common/port.h"
 #include "cartographer/mapping/probability_values.h"
-#include "cartographer/mapping/proto/submaps.pb.h"
+#include "cartographer/mapping/proto/submap_visualization.pb.h"
 #include "cartographer/mapping/trajectory_node.h"
 #include "cartographer/mapping_2d/probability_grid.h"
 #include "glog/logging.h"
diff --git a/cartographer/mapping/trajectory_node.cc b/cartographer/mapping/trajectory_node.cc
index ee560ca..c8d6d95 100644
--- a/cartographer/mapping/trajectory_node.cc
+++ b/cartographer/mapping/trajectory_node.cc
@@ -16,8 +16,6 @@
 
 #include "cartographer/mapping/trajectory_node.h"
 
-#include "cartographer/common/time.h"
-#include "cartographer/proto/trajectory.pb.h"
 #include "cartographer/transform/transform.h"
 
 namespace cartographer {
diff --git a/cartographer/mapping/trajectory_node.h b/cartographer/mapping/trajectory_node.h
index 6949e5d..9fe12ca 100644
--- a/cartographer/mapping/trajectory_node.h
+++ b/cartographer/mapping/trajectory_node.h
@@ -22,7 +22,7 @@
 
 #include "Eigen/Core"
 #include "cartographer/common/time.h"
-#include "cartographer/proto/trajectory.pb.h"
+#include "cartographer/mapping/proto/trajectory.pb.h"
 #include "cartographer/sensor/laser.h"
 #include "cartographer/transform/rigid_transform.h"
 
@@ -67,8 +67,7 @@ struct TrajectoryNodes {
   std::vector<mapping::TrajectoryNode> trajectory_nodes;
 };
 
-::cartographer::proto::Trajectory ToProto(
-    const std::vector<TrajectoryNode>& nodes);
+proto::Trajectory ToProto(const std::vector<TrajectoryNode>& nodes);
 
 }  // namespace mapping
 }  // namespace cartographer
diff --git a/cartographer/mapping_2d/CMakeLists.txt b/cartographer/mapping_2d/CMakeLists.txt
index 54fcfd9..342c453 100644
--- a/cartographer/mapping_2d/CMakeLists.txt
+++ b/cartographer/mapping_2d/CMakeLists.txt
@@ -150,7 +150,7 @@ google_library(mapping_2d_submaps
     mapping_2d_map_limits
     mapping_2d_probability_grid
     mapping_2d_proto_submaps_options
-    mapping_proto_submaps
+    mapping_proto_submap_visualization
     mapping_submaps
     mapping_trajectory_node
     sensor_laser
diff --git a/cartographer/mapping_2d/submaps.h b/cartographer/mapping_2d/submaps.h
index 2e8de6e..b152310 100644
--- a/cartographer/mapping_2d/submaps.h
+++ b/cartographer/mapping_2d/submaps.h
@@ -22,7 +22,7 @@
 
 #include "Eigen/Core"
 #include "cartographer/common/lua_parameter_dictionary.h"
-#include "cartographer/mapping/proto/submaps.pb.h"
+#include "cartographer/mapping/proto/submap_visualization.pb.h"
 #include "cartographer/mapping/submaps.h"
 #include "cartographer/mapping/trajectory_node.h"
 #include "cartographer/mapping_2d/laser_fan_inserter.h"
diff --git a/cartographer/mapping_3d/CMakeLists.txt b/cartographer/mapping_3d/CMakeLists.txt
index f854264..b624377 100644
--- a/cartographer/mapping_3d/CMakeLists.txt
+++ b/cartographer/mapping_3d/CMakeLists.txt
@@ -265,7 +265,7 @@ google_library(mapping_3d_submaps
     mapping_3d_hybrid_grid
     mapping_3d_laser_fan_inserter
     mapping_3d_proto_submaps_options
-    mapping_sparse_pose_graph
+    mapping_proto_submap_visualization
     mapping_submaps
     sensor_laser
     transform_transform
diff --git a/cartographer/mapping_3d/sparse_pose_graph/CMakeLists.txt b/cartographer/mapping_3d/sparse_pose_graph/CMakeLists.txt
index 0606f4b..e866bc3 100644
--- a/cartographer/mapping_3d/sparse_pose_graph/CMakeLists.txt
+++ b/cartographer/mapping_3d/sparse_pose_graph/CMakeLists.txt
@@ -53,7 +53,6 @@ google_library(mapping_3d_sparse_pose_graph_optimization_problem
     optimization_problem.h
   DEPENDS
     common_ceres_solver_options
-    common_lua_parameter_dictionary
     common_make_unique
     common_math
     common_port
@@ -64,6 +63,7 @@ google_library(mapping_3d_sparse_pose_graph_optimization_problem
     mapping_3d_rotation_cost_function
     mapping_3d_sparse_pose_graph_spa_cost_function
     mapping_3d_submaps
+    mapping_sparse_pose_graph
     mapping_sparse_pose_graph_proto_optimization_problem_options
     transform_transform
 )
diff --git a/cartographer/mapping_3d/sparse_pose_graph/optimization_problem.h b/cartographer/mapping_3d/sparse_pose_graph/optimization_problem.h
index 4ac4f5f..6d4eb34 100644
--- a/cartographer/mapping_3d/sparse_pose_graph/optimization_problem.h
+++ b/cartographer/mapping_3d/sparse_pose_graph/optimization_problem.h
@@ -24,9 +24,9 @@
 
 #include "Eigen/Core"
 #include "Eigen/Geometry"
-#include "cartographer/common/lua_parameter_dictionary.h"
 #include "cartographer/common/port.h"
 #include "cartographer/common/time.h"
+#include "cartographer/mapping/sparse_pose_graph.h"
 #include "cartographer/mapping/sparse_pose_graph/proto/optimization_problem_options.pb.h"
 #include "cartographer/mapping_3d/imu_integration.h"
 #include "cartographer/mapping_3d/submaps.h"
diff --git a/cartographer/mapping_3d/submaps.h b/cartographer/mapping_3d/submaps.h
index b6ac10a..e1cfe37 100644
--- a/cartographer/mapping_3d/submaps.h
+++ b/cartographer/mapping_3d/submaps.h
@@ -23,7 +23,7 @@
 
 #include "Eigen/Geometry"
 #include "cartographer/common/port.h"
-#include "cartographer/mapping/sparse_pose_graph.h"
+#include "cartographer/mapping/proto/submap_visualization.pb.h"
 #include "cartographer/mapping/submaps.h"
 #include "cartographer/mapping_2d/laser_fan_inserter.h"
 #include "cartographer/mapping_2d/probability_grid.h"
diff --git a/cartographer/proto/CMakeLists.txt b/cartographer/proto/CMakeLists.txt
deleted file mode 100644
index b86f7d8..0000000
--- a/cartographer/proto/CMakeLists.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 2016 The Cartographer Authors
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#      http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-google_proto_library(proto_trajectory
-  SRCS
-    trajectory.proto
-  DEPENDS
-    transform_proto_transform
-)
diff --git a/cartographer/transform/CMakeLists.txt b/cartographer/transform/CMakeLists.txt
index d3dd39d..15a820d 100644
--- a/cartographer/transform/CMakeLists.txt
+++ b/cartographer/transform/CMakeLists.txt
@@ -58,7 +58,7 @@ google_library(transform_transform_interpolation_buffer
   DEPENDS
     common_make_unique
     common_time
-    proto_trajectory
+    mapping_proto_trajectory
     transform_rigid_transform
     transform_transform
 )
diff --git a/cartographer/transform/transform_interpolation_buffer.cc b/cartographer/transform/transform_interpolation_buffer.cc
index b82930f..c8e9244 100644
--- a/cartographer/transform/transform_interpolation_buffer.cc
+++ b/cartographer/transform/transform_interpolation_buffer.cc
@@ -21,8 +21,6 @@
 #include "Eigen/Core"
 #include "Eigen/Geometry"
 #include "cartographer/common/make_unique.h"
-#include "cartographer/common/time.h"
-#include "cartographer/proto/trajectory.pb.h"
 #include "cartographer/transform/transform.h"
 #include "glog/logging.h"
 
@@ -87,10 +85,10 @@ bool TransformInterpolationBuffer::empty() const { return deque_.empty(); }
 
 std::unique_ptr<TransformInterpolationBuffer>
 TransformInterpolationBuffer::FromTrajectory(
-    const cartographer::proto::Trajectory& trajectory) {
+    const mapping::proto::Trajectory& trajectory) {
   auto interpolation_buffer =
       common::make_unique<TransformInterpolationBuffer>();
-  for (const cartographer::proto::Trajectory::Node& node : trajectory.node()) {
+  for (const mapping::proto::Trajectory::Node& node : trajectory.node()) {
     interpolation_buffer->Push(common::FromUniversal(node.timestamp()),
                                transform::ToRigid3(node.pose()));
   }
diff --git a/cartographer/transform/transform_interpolation_buffer.h b/cartographer/transform/transform_interpolation_buffer.h
index fda0b1f..d532527 100644
--- a/cartographer/transform/transform_interpolation_buffer.h
+++ b/cartographer/transform/transform_interpolation_buffer.h
@@ -21,7 +21,7 @@
 #include <memory>
 
 #include "cartographer/common/time.h"
-#include "cartographer/proto/trajectory.pb.h"
+#include "cartographer/mapping/proto/trajectory.pb.h"
 #include "cartographer/transform/rigid_transform.h"
 
 namespace cartographer {
@@ -31,7 +31,7 @@ namespace transform {
 class TransformInterpolationBuffer {
  public:
   static std::unique_ptr<TransformInterpolationBuffer> FromTrajectory(
-      const cartographer::proto::Trajectory& trajectory);
+      const mapping::proto::Trajectory& trajectory);
 
   // Adds a new transform to the buffer and removes the oldest transform if the
   // buffer size limit is exceeded.