Hi Defcon, the way you can do something like that is the external program can write out a .js script file that calls into MoI's API and then it can launch moi.exe giving it the path to the script file as a command line parameter.

When launched in that way MoI can be used to process files without showing any of the regular program UI.

There's an example for this type of batch file processing here:
http://kyticka.webzdarma.cz/3d/moi/#Batch

- Michael