Maybe move the question outside the loop? 
print "Delete files older than 3 days? [Y or N] \n";
chomp ($cleanup = <STDIN>);
if ($cleanup =~ /Y/i) {
   foreach my $file (@bigarray) {
    ...
   }
}

[download]

Untested!

Update:
Wow, you guys are *fast*! Two responses as I was typing my (meagre) thought....

In reply to Re: one user prompt instead of many by bibliophile
in thread one user prompt instead of many by AngusScrimm

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