I think that you can take photo of the biofilms and measure the intensity of the pixels. But you need to be careful with what is the reference.

Confocal laser scanning microscopy, after staining (for example, live/dead stain), is the easiest and advanced way to measure the thickness.

Light microscope also can be used and you can find more information in these papers:

http://www.sciencedirect.com/science/article/pii/016770129490006X

http://www.sciencedirect.com/science/article/pii/0167701286900059

and the protocol is explained here

http://www.hypertextbookshop.com/biofilmbook/v005/r001/Contents/02_Lab_Exercises/02_Protocols_and_Methods/02_Student_Version/09_Measurement_of_Biofilm_Thickness.html

Thanks. But my problem is my glass beads are a bit big. about 0.25 mm. And it difficult veiwing them on CLSM. I was looking for a gravimetric method. I found only one literature on it. but was looking if some one has more information about it.