Perl arrays start with an index of 0. That is, the first element of @items can be accessed as $items[0]. Adding a blank element to the start of the array means that if the user requests file 1, you can just say @user_files[$choice] instead of $user_files[$choice - 1].

I'd rather do $choice - 1, but either way, add a comment to the code noting your choice and why you're doing it:

# @user_files starts at zero, user choice starts at 1
process($user_files[$choice - 1]);
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That'll make life much easier for the maintainer.