How do we extract the etchant after it is stopped at the boron layer in MEMs fabrication process?
If you are performing a wet etch you use some other liquid, usually water, to remove residual etchant. Substrates will be in some etchant bath for the required amount of time, once that time is complete they are transferred to a rinse tank to stop the etch and remove residual etch chemicals. 

Dry etches are done in a vacuum chamber. When the etch is complete, the etchant gases are pumped out with a vacuum pump.