Dear Sanaz ;

You said bacterial cell-free supernatant. bacterial cell-free supernatant has no CFU (colony forming unit) the unit used to estimate the number of viable bacteria cells in a sample. May be if you are interested in cell-free supernatant, you need to study the secondary metabolites produced by the bacteria. in supernatant, you can find these secondary metabolites and use it for your study. But if you are still concerned with CFU, use centrifuge to separate viable bacterial cell and supernatant and discard the supernatant. Then used any CFU counting available method in your laboratory (like spectrometer).