fig and m files (and other purely MATLAB and Toolbox functionality) can be converted to a standalone app using

a product called the "MATLAB Compiler". However, the MATLAB Compiler does _not_ support _any_ Simulink (or Blockset) functionality. The mechanism to convert a Simulink model to standalone code is the product called "Real-Time Workshop" (or RTW for short). Unfortunately there is no single/simple method to convert a combined MATLAB and Simulink application to a standalone application. You can however use the following process: 1. Convert your Simulink model to a standalone exe using the RSIM target of RTW 2. Rewrite your UI to use the appropriate MATLAB functions for manipulating the RSIM generated exe (which with a little work allows you to run the model, tune parameters, and retrieve resulting data). 3. Use the MATLAB Compiler to convert the UI created in step 2 to a standalone exe. You then have 2 exe's that can work with each other.