You need to accumulate the list first, then ask the user in case there are any entries, and delete them if so.

my @everyfile = (
    glob( "C:/input/*.htm" ),
    glob( "C:/input/*.doc" ),
    glob( "C:/input/*.pdf" ),
);

my @oldfile = grep -M > 3, @everyfile;

if( @oldfile ) {
    print "Delete files older than 3 days?  [Y or N] \n";
    chomp( $cleanup = <STDIN> );
    if( $cleanup =~ /Y/i ) {
        unlink @oldfile;
    }
    else {
        print "\n      <<No files deleted at this time>>\n";
    }
}
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Note that you can pass multiple files to unlink. Don't loop.

Makeshifts last the longest.