Err..., a substring between two adjacent characters is always "".

Probably, not the best title chosen for your problem.

As said, a regex solves your problem easily:

while (<DATA>){
    if (/^.*?\_(.*?)(CI|I)SD\_.*?$/)
          {print $1,"\n"}
}
__DATA__
my_firstmachISD_blah_blah
the_secondCISD_blah_blah_blah
[download]

Updated: I need to trim the last few characters which could be either CISD or ISD

Updated again: yes, C?ISD is better than (CI|I)SD