Certainly, however there are some things to consider. If the program in discussion is run from a DOS prompt (meaning, it's a DOS based program, so, it shouldn't really have a "windows" window.), then you'll have to get creative. DOS Prompts, in my experience don't work well with sendkeys, so you would need to copy the data to the clipboard, and then send an "alt space ep" ("% ep", which is alt, space, e [for edit] and p [for paste]) to paste the data from the clipboard to the DOS prompt or DOS Based Program.
If you are working in a windows based program, for example, transfering data from excel to quicken or something crazy, you could absolutely create an instance of the excel object, load the spreadsheet of your choice, read in the data from the cells, and transfer that information to another windows based program no problem. Let me know if you need any further assistance in this matter.