diff --git a/README.md b/README.md
index 97a8f845..1f2926d8 100644
--- a/README.md
+++ b/README.md
@@ -32,7 +32,7 @@ OpenDroneMap can run natively on Ubuntu 14.04 or later, see [Build and Run Using
 Current version: 0.2 (this software is in beta)
 
 1. Extract and enter the OpenDroneMap directory
-2. Run `bash configure.sh`
+2. Run `bash configure.sh install`
 4. Copy the default settings file and edit it: `cp default.settings.yaml settings.yaml`. Set the `project-path` value to an empty directory (you will place sub-directories containing individual projects inside). You can add many options to this file, [see here](https://github.com/OpenDroneMap/OpenDroneMap/wiki/Run-Time-Parameters)
 3. Download a sample dataset from [here](https://github.com/OpenDroneMap/odm_data_aukerman/archive/master.zip) (about 550MB) and extract it as a subdirectory in your project directory.
 4. Run `./run.sh odm_data_aukerman` 
@@ -47,7 +47,13 @@ See [here](https://github.com/OpenDroneMap/OpenDroneMap/tree/ebaaf802a1fb50e335b
 
 Extract and enter the downloaded OpenDroneMap directory and compile all of the code by executing a single configuration script:
   
-    bash configure.sh
+    bash configure.sh install
+    
+When updating to a newer version of ODM, it is recommended that you run 
+
+    bash configure.sh reinstall
+    
+to ensure all the dependent packages and modules get updated.  
 
 For Ubuntu 15.10 users, this will help you get running:
 
diff --git a/configure.sh b/configure.sh
index 67aba83a..fc9a30e9 100755
--- a/configure.sh
+++ b/configure.sh
@@ -1,95 +1,134 @@
 #!/bin/bash
 
-## Set up library paths
-RUNPATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-export PYTHONPATH=$RUNPATH/SuperBuild/install/lib/python2.7/dist-packages:$RUNPATH/SuperBuild/src/opensfm:$PYTHONPATH
-export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RUNPATH/SuperBuild/install/lib
+install() {
+    ## Set up library paths
 
-## Before installing
-echo "Updating the system"
-sudo apt-get update
+    export PYTHONPATH=$RUNPATH/SuperBuild/install/lib/python2.7/dist-packages:$RUNPATH/SuperBuild/src/opensfm:$PYTHONPATH
+    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RUNPATH/SuperBuild/install/lib
 
-sudo add-apt-repository -y ppa:ubuntugis/ppa
-sudo apt-get update
+    ## Before installing
+    echo "Updating the system"
+    sudo apt-get update
 
-echo "Installing Required Requisites"
-sudo apt-get install -y -qq build-essential \
-                     git \
-                     cmake \
-                     python-pip \
-                     libgdal-dev \
-                     gdal-bin \
-                     libgeotiff-dev \
-                     pkg-config
+    sudo add-apt-repository -y ppa:ubuntugis/ppa
+    sudo apt-get update
 
-echo "Getting CMake 3.1 for MVS-Texturing"
-sudo apt-get install -y software-properties-common python-software-properties
-sudo add-apt-repository -y ppa:george-edison55/cmake-3.x
-sudo apt-get update -y
-sudo apt-get install -y --only-upgrade cmake
+    echo "Installing Required Requisites"
+    sudo apt-get install -y -qq build-essential \
+                         git \
+                         cmake \
+                         python-pip \
+                         libgdal-dev \
+                         gdal-bin \
+                         libgeotiff-dev \
+                         pkg-config
 
-echo "Installing OpenCV Dependencies"
-sudo apt-get install -y -qq libgtk2.0-dev \
-                     libavcodec-dev \
-                     libavformat-dev \
-                     libswscale-dev \
-                     python-dev \
-                     python-numpy \
-                     libtbb2 \
-                     libtbb-dev \
-                     libjpeg-dev \
-                     libpng-dev \
-                     libtiff-dev \
-                     libjasper-dev \
-                     libflann-dev \
-                     libproj-dev \
-                     libxext-dev \
-                     liblapack-dev \
-                     libeigen3-dev \
-                     libvtk5-dev
+    echo "Getting CMake 3.1 for MVS-Texturing"
+    sudo apt-get install -y software-properties-common python-software-properties
+    sudo add-apt-repository -y ppa:george-edison55/cmake-3.x
+    sudo apt-get update -y
+    sudo apt-get install -y --only-upgrade cmake
 
-echo "Removing libdc1394-22-dev due to python opencv issue"
-sudo apt-get remove libdc1394-22-dev
+    echo "Installing OpenCV Dependencies"
+    sudo apt-get install -y -qq libgtk2.0-dev \
+                         libavcodec-dev \
+                         libavformat-dev \
+                         libswscale-dev \
+                         python-dev \
+                         python-numpy \
+                         libtbb2 \
+                         libtbb-dev \
+                         libjpeg-dev \
+                         libpng-dev \
+                         libtiff-dev \
+                         libjasper-dev \
+                         libflann-dev \
+                         libproj-dev \
+                         libxext-dev \
+                         liblapack-dev \
+                         libeigen3-dev \
+                         libvtk5-dev
 
-## Installing OpenSfM Requisites
-echo "Installing OpenSfM Dependencies"
-sudo apt-get install -y -qq python-networkx \
-                     libgoogle-glog-dev \
-                     libsuitesparse-dev \
-                     libboost-filesystem-dev \
-                     libboost-iostreams-dev \
-                     libboost-regex-dev \
-                     libboost-python-dev \
-                     libboost-date-time-dev \
-                     libboost-thread-dev \
-                     python-pyproj
+    echo "Removing libdc1394-22-dev due to python opencv issue"
+    sudo apt-get remove libdc1394-22-dev
 
-sudo pip install -U PyYAML \
-                    exifread \
-                    gpxpy \
-                    xmltodict \
-                    appsettings
+    ## Installing OpenSfM Requisites
+    echo "Installing OpenSfM Dependencies"
+    sudo apt-get install -y -qq python-networkx \
+                         libgoogle-glog-dev \
+                         libsuitesparse-dev \
+                         libboost-filesystem-dev \
+                         libboost-iostreams-dev \
+                         libboost-regex-dev \
+                         libboost-python-dev \
+                         libboost-date-time-dev \
+                         libboost-thread-dev \
+                         python-pyproj
 
-echo "Installing Ecto Dependencies"
-sudo pip install -U catkin-pkg
-sudo apt-get install -y -qq python-empy \
-                     python-nose \
-                     python-pyside
+    sudo pip install -U PyYAML \
+                        exifread \
+                        gpxpy \
+                        xmltodict \
+                        appsettings
 
-echo "Installing OpenDroneMap Dependencies"
-sudo apt-get install -y -qq python-pyexiv2 \
-                     python-scipy \
-                     jhead \
-                     liblas-bin 
+    echo "Installing Ecto Dependencies"
+    sudo pip install -U catkin-pkg
+    sudo apt-get install -y -qq python-empy \
+                         python-nose \
+                         python-pyside
 
-echo "Compiling SuperBuild"
-cd SuperBuild
-mkdir -p build && cd build
-cmake .. && make -j$(nproc)
+    echo "Installing OpenDroneMap Dependencies"
+    sudo apt-get install -y -qq python-pyexiv2 \
+                         python-scipy \
+                         jhead \
+                         liblas-bin
 
-echo "Compiling build"
-cd ../..
-mkdir -p build && cd build
-cmake .. && make -j$(nproc)
+    echo "Compiling SuperBuild"
+    cd ${RUNPATH}/SuperBuild
+    mkdir -p build && cd build
+    cmake .. && make -j$(nproc)
 
-echo "Configuration Finished"
+    echo "Compiling build"
+    cd ${RUNPATH}
+    mkdir -p build && cd build
+    cmake .. && make -j$(nproc)
+
+    echo "Configuration Finished"
+}
+
+uninstall() {
+    echo "Removing SuperBuild and build directories"
+    cd ${RUNPATH}/SuperBuild
+    rm -rfv build src download install
+    cd ../
+    rm -rfv build
+}
+
+reinstall() {
+    echo "Reinstalling ODM modules"
+    uninstall
+    install
+}
+
+usage() {
+    echo "Usage:"
+    echo "bash configure.sh <install|update|uninstall|help>"
+    echo "Subcommands:"
+    echo "  install"
+    echo "    Installs all dependencies and modules for running OpenDroneMap"
+    echo "  reinstall"
+    echo "    Removes SuperBuild and build modules, then re-installs them. Note this does not update OpenDroneMap to the latest version. "
+    echo "  uninstall"
+    echo "    Removes SuperBuild and build modules. Does not uninstall dependencies"
+    echo "  help"
+    echo "    Displays this message"
+}
+
+if [[ $1 =~ ^(install|reinstall|uninstall|usage)$ ]]; then
+    RUNPATH="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+    "$1"
+else
+    echo "Invalid instructions." >&2
+    usage
+    exit 1
+fi
\ No newline at end of file