diff --git a/.gitignore b/.gitignore
index 7f6a4445f3..ebfcf22cce 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,8 +20,9 @@
 Archives/*
 Build/*
 Testing/
-Binaries/*
-Meta/*
+Packages/*
+s3deploy-branch/
+s3deploy-archive/
 build/*
 build_*/
 core
diff --git a/.travis.yml b/.travis.yml
index a2cb7e9d83..c75ae3dee0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -78,9 +78,7 @@ script:
 after_success:
   - if [[ "${TRAVIS_OS_NAME}" = "linux" && "${TRAVIS_BRANCH}" != "coverity" ]]; then
          make package_firmware && mkdir s3deploy-archive && cp Firmware.zip s3deploy-archive/
-      && cp Binaries/* .
-      && find . -maxdepth 1 -mindepth 1 -type f -name 'nuttx-*-default.px4' | sed 's/.\/nuttx-//' | sed 's/-default.px4//' | xargs -I{} mv nuttx-{}-default.px4 {}_default.px4
-      && mkdir s3deploy-branch && mv *_default.px4 Meta/px4fmu-v4_default/parameters.xml Meta/px4fmu-v4_default/airframes.xml s3deploy-branch/;
+      && Tools/s3_deploy.py;
     fi
   - if [[ "${TRAVIS_OS_NAME}" = "linux" && "$GCC_VER" == "5.4" && "${TRAVIS_BRANCH}" != "coverity" ]]; then
       export PX4_S3_DEPLOY=1;
diff --git a/Makefile b/Makefile
index f766e79cd5..02e08069c4 100644
--- a/Makefile
+++ b/Makefile
@@ -300,7 +300,7 @@ clang-tidy:
 	@$(SRC_DIR)/Tools/clang-tool.sh -b build_posix_sitl_default -t clang-tidy
 
 package_firmware:
-	@zip --junk-paths Firmware.zip `find Binaries/. -name \*.px4`
+	@./Tools/package_firmware.py
 
 clean:
 	@rm -rf build_*/
diff --git a/Tools/package_firmware.py b/Tools/package_firmware.py
new file mode 100755
index 0000000000..338d41ded3
--- /dev/null
+++ b/Tools/package_firmware.py
@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+
+import glob
+import zipfile
+import os
+
+FIRMWARE_FILE = 'Firmware.zip'
+
+
+def extract_file_only(filename, dest):
+    """
+    Extract a file without keeping directories.
+    """
+    # extract firmware files without paths
+    f_src = archive.open(filename, 'r')
+    data = f_src.read()
+    dst_name = os.path.join(dest, os.path.basename(filename))
+    with open(dst_name, 'w') as f_dst:
+        f_dst.write(data)
+    f_src.close()
+
+# open destination archive
+with zipfile.ZipFile(FIRMWARE_FILE, 'w') as dest_archive:
+
+    # get all zip files in Packages directory
+    for zip_filename in glob.glob("Packages/*.zip"):
+
+        # open zipfile
+        with zipfile.ZipFile(zip_filename, 'r') as archive:
+
+            # look for interesting names
+            for src_filename in archive.namelist():
+
+                # extract firmware files
+                if os.path.splitext(src_filename)[1] == '.px4':
+                    base_name = os.path.basename(src_filename)
+                    dest_archive.writestr(base_name, archive.read(src_filename))
diff --git a/Tools/s3_deploy.py b/Tools/s3_deploy.py
new file mode 100755
index 0000000000..3013a0952d
--- /dev/null
+++ b/Tools/s3_deploy.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+import glob
+import zipfile
+import os
+import re
+import shutil
+
+S3_DIR = 's3deploy-branch'
+S3_ARCHIVE_DIR = 's3deploy-branch'
+
+if not os.path.isdir(S3_DIR):
+    os.mkdir(S3_DIR)
+
+if not os.path.isdir(S3_ARCHIVE_DIR):
+    os.mkdir(S3_ARCHIVE_DIR)
+
+shutil.copyfile(Firmware.zip, S3_ARCHIVE_DIR)
+
+def extract_file_only(filename, dest):
+    # extract firmware files without paths
+    f_src = archive.open(filename, 'r')
+    data = f_src.read()
+    with open(os.path.join(dest,
+              os.path.basename(filename)), 'w') as f_dst:
+        f_dst.write(data)
+    f_src.close()
+
+# get all zip files in Packages directory
+for zip_filename in glob.glob("Packages/*.zip"):
+
+    # open zipfile
+    with zipfile.ZipFile(zip_filename, 'r') as archive:
+
+        # look for interesting names
+        for filename in archive.namelist():
+
+            # extract firmware files
+            if os.path.splitext(filename)[1] == '.px4':
+                extract_file_only(filename, S3_DIR)
+
+            # copy px4fmu-v4_default xml files for qgroundcontrol
+            if re.match(filename, r'.*px4fmu-v4_default.*\.xml') is not None:
+                extract_file_only(filename, S3_DIR)