Automating search and replace in a third party program

[JerryS]

I have many files that I need to search and replace multiple terms within.  I have made a CSV file that contains two columns.  The first column contains the term I need to search for and the second column contains the item that will replace the search term.  For example:

Column 1 (search term)             Column 2 (replace term)
foo                                                 boo
gravy                                             train

I have found utilities that provide this kind of "batch" search and replace functionality across multiple files such as "Advanced Find and Replace".  Unfortunately, these programs only work for text based files, not for proprietary file formats such as what I am working with.  The files I am working with open in a program that allows me to edit the files.  There is even a search and replace function in the program, but I have to search and replace one term at a time.  My CSV file that contains my search and replace terms contains about 3000 unique items, which makes this a tedious and slow process.  What I am trying to accomplish is to write a script that interacts with the program that can open the files by automating the search and replace function inside that program using the terms in the CSV file I have created.  I am not sure if AutoIT is the right scripting tool to provide this kind of functionality.  Any help or guidance is much appreciated.  Thank you!