Imaging and automated cell counting are the most common methods of biofilm quantification. Furthermore, the use of stains or fluorescent markers, in order to more accurately identify cells of interest and distinguish from culture debris, allow for easier and increased accuracy of cell counting and data interpretation.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6133255/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079648/

with biofilm measurements in general and saw using SEM

You would need to remove the biofilm in a way that does not cause damage to the underlying substrate, then use imaging eg SEM to examine the surface topography. You could measure pitting using atomic force microscopy.