AP160 and AP161 Check file

Do you mean changing AP160/AP161 code to produce a different output file, or changing the file once it has been created (i.e. post-processing).

I'm not really sure what i need to change... I guess i need to change the code to modify the output file.

It will be better if you modify the Program / Code so you don't modify data. Modifying data is BAD.
You can also use a third party software to READ the standard output, and format / add / delete data you need.

would it be possible for you to post 2 or 3 lines of standard output and then those lines modified? Then we can offer more precise opinions.

Jonathan, it really depends on what it is you're trying to accomplish. If you just trying to add headers/footers, etc. for submission to the bank, etc. I would do it as a post-processing script which runs after AP160/AP161. That way you don't have to maintain a customized copy of the program. However, if you're trying to implement a new format (CLIEOP, for instance) that would probably require one of two options:

1) take the output of AP160/AP161 and run it through some data transformation tool, like Mercator/DataStage, etc. assuming you have such a tool and/or expertise to support it, or

2) clone AP160 and modify the cloned version to generate the desired output. This would require periodic retrofits of new CTP/MSP patches to AP160 into your customized version.