If a bank's assessment area extends substantially beyond the boundaries of an MSA, separate assessment areas should be establised. You need to understand what examiners are saying. Are they saying that the assessment area is not set up properly and should be established as multiple assessment areas, or that overall the area is too large for the bank to handle?
I am still seeing wildly different viewpoints from examiners even from the same agency on whole counties vs partial counties.
Re an MSA, yes, you can select an MSA as the assessment area if that is appropriate,
Refer to the q and a at
http://www.ffiec.gov/cra/pdf/2010-4903.pdfThe discussion on assessment areas starts around page 11666.