We're an ISO9001-2000 certified company working towards CMMI ML 3. Can we be certified in our software department only?
There is a concept in the SCAMPI Appraisal process called the "organizational unit," or "OU." The OU is the targeted organization to be appraised and must be a logical entity or grouping of some kind. This could include: All Web Development Teams, The Project Management Office, and yes, the Software Department. You will need to discuss this with your Lead Appraiser to ensure his/her understanding of your request, but I see no reason that you could not appraise just this part of your company.