I think we need a bit more information on your specific case. Do you want to store the filehandles into the array of arrays, or would your prefer to store the actual file contents? Remember that if you are working with large files and you store the entire file into the array, you're talking about utilizing a great deal of memory.

If these are text files, I'd choose a hash of filehandles. If you had fully-qualified paths to all your files in the array @files, I'd do something like this:

my %filehandles;
open $filehandles{$_}, $_ for @files;
[download]

Then you can work with each individual filehandle as you wish, and everything is indexed by the file's name. Note that this is only one solution. There are lots of ways to approach this question.