@ARGV is the array of command line arguments (see perlvar .. and they would not normally need to be chomped). If you want to prompt the user for arguments, you can use:

print "Enter directory: ";
chomp(my $dir = <STDIN>);
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Or you might try IO::Prompt. For searching subdirectories, you can use File::Find. You are automatically chdir'd to the directory of each file as it is 'found'.