diff --git a/lib/gltfPipeline.js b/lib/gltfPipeline.js
index 866882b6..2dba0f15 100644
--- a/lib/gltfPipeline.js
+++ b/lib/gltfPipeline.js
@@ -1,4 +1,5 @@
 'use strict';
+var async = require('async');
 var addDefaults = require('./addDefaults');
 var addPipelineExtras = require('./addPipelineExtras');
 var removeUnused = require('./removeUnused');
@@ -16,6 +17,7 @@ var loadGltfUris = require('./loadGltfUris');
 var quantizeAttributes = require('./quantizeAttributes');
 var cacheOptimizeIndices = require('./cacheOptimizeIndices');
 var encodeImages = require('./encodeImages');
+var writeSource = require('./writeSource');
 var Cesium = require('cesium');
 var defaultValue = Cesium.defaultValue;
 
@@ -26,13 +28,27 @@ module.exports = {
     processFileToDisk : processFileToDisk
 };
 
+function writeSources(gltf, callback) {
+    var embed = true;
+    var embedImage = true;
+    async.each(['buffers', 'images', 'shaders'], function(name, asyncCallback) {
+        writeSource(gltf, undefined, name, embed, embedImage, asyncCallback);
+    }, function() {
+        callback();
+    });
+}
+
 function processJSON(gltf, options, callback) {
     addPipelineExtras(gltf);
     loadGltfUris(gltf, options, function(err, gltf) {
         if (err) {
             throw err;
         }
-        processJSONWithExtras(gltf, options, callback);
+        processJSONWithExtras(gltf, options, function(gltf) {
+            writeSources(gltf, function() {
+                callback(gltf);
+            });
+        });
     });
 }
 
@@ -71,7 +87,9 @@ function processJSONWithExtras(gltfWithExtras, options, callback) {
 function processFile(inputPath, options, callback) {
     readGltf(inputPath, options, function(gltf) {
         processJSONWithExtras(gltf, options, function(gltf) {
-            callback(gltf);
+            writeSources(gltf, function() {
+                callback(gltf);
+            });
         });
     });
 }
@@ -89,14 +107,22 @@ function writeFile(gltf, outputPath, options, callback) {
 }
 
 function processJSONToDisk(gltf, outputPath, options, callback) {
-    processJSON(gltf, options, function(gltf) {
-        writeFile(gltf, outputPath, options, callback);
+    addPipelineExtras(gltf);
+    loadGltfUris(gltf, options, function(err, gltf) {
+        if (err) {
+            throw err;
+        }
+        processJSONWithExtras(gltf, options, function(gltf) {
+            writeFile(gltf, outputPath, options, callback);
+        });
     });
 }
 
 function processFileToDisk(inputPath, outputPath, options, callback) {
-    processFile(inputPath, options, function(gltf) {
-        writeFile(gltf, outputPath, options, callback);
+    readGltf(inputPath, options, function(gltf) {
+        processJSONWithExtras(gltf, options, function(gltf) {
+            writeFile(gltf, outputPath, options, callback);
+        });
     });
 }
 
diff --git a/lib/writeGltf.js b/lib/writeGltf.js
index 8932fe2c..9f59ab30 100755
--- a/lib/writeGltf.js
+++ b/lib/writeGltf.js
@@ -9,7 +9,7 @@ var removePipelineExtras = require('./removePipelineExtras');
 module.exports = writeGltf;
 
 function writeGltf(gltf, outputPath, embed, embedImage, createDirectory, callback) {
-    //Create the output directory if specified
+    // Create the output directory if specified
     if (createDirectory) {
         outputPath = path.join(path.dirname(outputPath), 'output', path.basename(outputPath));
     }
diff --git a/lib/writeSource.js b/lib/writeSource.js
index 4468a821..a57c2d42 100644
--- a/lib/writeSource.js
+++ b/lib/writeSource.js
@@ -14,7 +14,7 @@ module.exports = writeSource;
 function writeSource(gltf, basePath, name, embed, embedImage, callback) {
     var objects = gltf[name];
 
-    //Iterate through each object and write out its uri
+    // Iterate through each object and write out its uri
     if (defined(objects)) {
         var ids = Object.keys(objects);
         async.each(ids, function(id, asyncCallback) {
@@ -24,7 +24,7 @@ function writeSource(gltf, basePath, name, embed, embedImage, callback) {
                 var extension = object.extras._pipeline.extension;
 
                 // Write the source object as a data or file uri depending on the embed flag
-                if (embed && (embedImage || name !== 'images')) {
+                if (embed && (embedImage || name !== 'images') || !defined(basePath)) {
                     var sourceDataUri = new dataUri();
                     if (name === 'shaders') {
                         sourceDataUri.format('.txt', source);
diff --git a/specs/lib/gltfPipelineSpec.js b/specs/lib/gltfPipelineSpec.js
index e5394b0c..bbe92a4f 100644
--- a/specs/lib/gltfPipelineSpec.js
+++ b/specs/lib/gltfPipelineSpec.js
@@ -107,8 +107,33 @@ describe('gltfPipeline', function() {
             createDirectory : false
         };
         readGltf(gltfPath, options, function(gltf) {
+            var options = { basePath : path.dirname(gltfPath) };
             processJSONToDisk(gltf, outputPath, options, function() {
-                expect(path.normalize(spy.calls.first().args[0])).toEqual(path.normalize('./output/'));
+                expect(path.normalize(spy.calls.first().args[0])).toEqual(path.normalize('output/output'));
+                done();
+            });
+        });
+    });
+
+    it('will write sources from JSON', function(done) {
+        var options = {};
+        readGltf(gltfEmbeddedPath, options, function (gltf) {
+            var initialUri = gltf['buffers'].CesiumTexturedBoxTest.uri;
+            processJSON(gltf, options, function () {
+                var finalUri = gltf['buffers'].CesiumTexturedBoxTest.uri;
+                expect(initialUri).not.toEqual(finalUri);
+                done();
+            });
+        });
+    });
+
+    it('will write sources from file', function(done) {
+        var options = {};
+        readGltf(gltfEmbeddedPath, options, function (gltf) {
+            var initialUri = gltf['buffers'].CesiumTexturedBoxTest.uri;
+            processFile(gltfEmbeddedPath, options, function (gltfFinal) {
+                var finalUri = gltfFinal['buffers'].CesiumTexturedBoxTest.uri;
+                expect(initialUri).not.toEqual(finalUri);
                 done();
             });
         });
@@ -116,10 +141,9 @@ describe('gltfPipeline', function() {
 
     it('will add image processing extras if this is a pipeline with image processing', function(done) {
         var options = {
-            imageProcess: true
+            imageProcess : true
         };
         readGltf(gltfEmbeddedPath, options, function(gltf) {
-            var gltfCopy = clone(gltf);
             processJSON(gltf, options, function (gltf) {
                 expect(gltf).toBeDefined();
                 var images = gltf.images;