See system call with time out. There are other ways too, if you want to use an event loop, or thread for a timer, but alarm is usually what you are after. An old example:

#!/usr/bin/perl
use strict;
use warnings;

my $timeout = 180;
my @array = (
        "command 1 goes here",
        "command 2 goes here",
        "command 3 goes here",
        );

for (@array) {
eval {
    local $SIG{ALRM} = sub {
        die "alarm\n";
    };
    alarm $timeout;
    system($_);
    alarm 0;
  };

}

# abigail says
# Don't do it with system directly, or you might generate zombies. 
# fork(), do an exec() in the child, and then, in an eval block, 
# setup an alarm handler that does a die(), set the alarm, 
# waitpid() for your child, cancel the alarm. Outside the eval 
# block, check for $@, if it indicates the alarm was triggered, 
# kill the child and waitpid() for it.
# No doubt there are some race conditions left in, but it's a start.
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