Для удаления perl модулей удобно использовать pm-uninstall. Для этого с помощью cpan устанавливаем App::pmuninstall

cpan[1]> install App::pmuninstall
Reading '/root/.cpan/Metadata'
Database was generated on Mon, 04 Apr 2016 12:29:02 GMT
Fetching with LWP:
http://www.cpan.org/authors/01mailrc.txt.gz
Reading '/root/.cpan/sources/authors/01mailrc.txt.gz'

pm-uninstall --help
Usage:
      pm-uninstall [options] Module ...

      options:
          -v,--verbose                  Turns on chatty output
          -f,--force                    Uninstalls without prompts
          -c,--checkdeps                Check dependencies ( default on )
          -n,--no-checkdeps             Not check dependencies
          -h,--help                     This help message
          -V,--version                  Show version
          -l,--local-lib                Additional module path
          -L,--local-lib-contained      Additional module path (don't include non-core modules)

Пример удаления модуля DBD::mysql  :

$ pm-uninstall DBD::mysql