That's a good way to store the data structure (I was going to reply and suggest a hashref of arrayrefs). I'd just like to add a caveat: be careful, slurping an entire file into memory can be a bad idea if the file is too big -- especially if you're going to manipulate the data.

A better bet may be to create an array of filehandles, append the data to each filehandle, and the reread in to reduce the total amount of memory you're going to need.