After they are dry, you can cut the filter for suitable size to be mounted on a SEM-stud, whereafter they have to be coated for conductivity. Obviously, you still loose internal specimen detail because of ice crystal growth but a considerable amount of external detail is successfully preserved. The authors present a number of good SEM images. Whether the procedure will work successfully with specimens as small as bacteria, I'm not sure. We have resorted to exposure to osmium vapors for an extended period such as 24-72 hours and then air drying.
Some bacteria can stand airdrying.
I suggest trying this with part of the sample. If the bacteria or other organisms look deflated you can CPD the remainder. There are several kinds of filters. Other ones are a torturous path type and it will be hard to find the bacteria on them. Polycarbonate ones are smooth with round holes in them.