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use Symbol 'delete_package';
foreach my $module (@modules) {
   require "sub/$module.pm";
...
   #cleanup
   delete_package($module);
}

use Symbol 'delete_package';
foreach my $module (@modules) {
...
   #cleanup
   delete_package($module);
}

use Symbol 'delete_package';
require UNIVERSAL::require;
...
   #cleanup
   delete_package($module);
}