After running stain only one well and keeping it as reference, cut out your protein in other wells. Homogenize the cut pieces of gel and centrifuge at 10000 rpm and in supernatant you get your protein.
First step is to locate the electrophoresed protein in the gel (Visualization of the protein in the gel using Stain), secondly remove the SDS from the sample and at last renature your protein. The process of protein extraction from gels can be done by dissolution of the gel matrix.