If your program needs to scan the data multiple times each time you run it and you have the memory to spare to hold the whole file in memory (almost certainly w/ a file as small as 6000x7) then by all means read the file in once and store it in an array (or other data structure) and process off of that. If you are only going to need to scan the data once each time your program is run then you will see no over-all preformance gains by pre-loading it into memory.

One module you may want to check out is Text::CSV. It provides parsing for CSV formatted files.