This can be done but the ease at which it can be done depends on the format of your data.
Are all the locations in the same file? ie the origins and their associated destinations or are they in separate files.
or are the origins in one file and all the destinations in another file which has a key to associate each destination with one origin?
Are all the files in a projected coordinate system?
Do they cover great distances (ie 10's, 100's 1000's of kilometers)
Any substantive information on the existing data structures and input coordinate systems would be helpful.