You can follow Conde's strategy with considering other filter systems. Some centrifuge tubes have their own filter system based on size.

If you think lyzse your cells you can use any surfactant agents (Tweens, SDS) that disrupt/lyse the cell membrane and then sonicate the cells. By this way you can get more NPs free.

You can try adding triton x-100 0.1% in water and sonicating for 1 hour.

I totally agree with all these answers and what i suggest is to sonicate the samples with the Triton and then try to centrifuge and get the bottom layer which might have your gold or silver particles. If your particles have any charge on it, try to use gel electrophoresis set up for further isolation. It will help you even you have different sizes of nano particles.

Try to lyse the cells using water. Due to low osmolarity of water, the cells will swell and burst. Then if you still that see some of the cells are intact, you can try freeze thaw cycles. I anticipate at most a couple of freeze thaw cycles will definitely burst the remaining cells. The reason I am not recommending any ionic substance is potential aggregation of your nanoparticles as you are not sure what surface charge they will have. Once you lyse the cells, you can separate them from the cell debris using filtration, regular centrifugation or density gradient centrifugation.

Thank you every one, really appreciate the help.

@ Pratixa Joshi; You said its better not to use ionic detergents as I have no idea about the surface charge, that is correct but you think I can try with ionic detergents?

if you want isolate pure nanoparticles centrifuge 2-3 times and wash with sterilized distilled water and collect the pellet to dry ..now u can characterize with TEM or XRD you get good results.

I wish to make carbon or silver nanoparticles from secondary metabolites of the plants,plz suggests me the procedure