Pretty sure you can't really run an unmanaged program in a C# sandbox, save for writing an unmanaged emulator in C# and running the unmanaged executable in that. And it'd be slow to run and hard to write so you probably don't want to go that route.
The only way I could see this working would be if the unmanaged program called a C# wrapper for the file system. Do you have the source code for the unmanaged program?