print uc("abcõäöüšž"), "\n";
Wait a sec, š and ž aren't found in iso-8859-1. The file you describe can't possibly exist. If the file is encoded using an encoding other than iso-8859-1, you need to tell Perl. use utf8; tells Perl that the source is encoded using UTF-8.
That applies to the OP of this thread too, although it won't change the outcome.
# Source is UTF-8
# Appropriate de/encode data going through STDIN/OUT/ERR.
use open ':std', ':locale';