Well, the answer to your original question will depend largely on what language the applications are written in.
For instance, if the applications are operating system dependent, meaning they must run under a specific operating system like WINDOWS, then they are probably written in a language like C or C++ or similar language and they have probably been compiled into an EXE file with supporting DLL files.
And the only way to change the code would be to have the original code before it was compiled, make the changes and then recompile it.
But if the programs are internet based, they may be output as HTML.
If they are interactive, then they will be written in a language like ASP, PHP, PERL or any number of other scripting languages.
If this is the case, then modifying them will be much easier.
So as you can see, without more specific information, there is very little that anyone can do for you.