You may get better marks if you populated a hash with the filename / directory pairs since this could be populated from a configuration file.

my %destinations = qw(
file1 sysbacks
file2 alpha
file3 gamma/blue
file4 gamma/green
file5 gamma/green
);

#later

my $target = "$destinations{$filename}/$filename";
[download]

I take your point about making his professor believe it was him. Even this code is too well written for a newbie. Try the following newbie style tips...

1. Remove the elsif and hust have a bunch of if statements one after the other.
2. Use a regex for the if test but manually assign $_ = $file beforehand.
3. chomp the input on the way in.
4. Use the $_ explicitly in the print statement with a newline to make up for the chomp!
5. Use a different variable to store the name of the output file.