Safety first! Start by wearing proper gloves and safety glasses for handling and removing the damaged glass. Now, remove any broken pieces of glass from the window frame. Keep in mind that the broken glass will be very sharp and should be disposed of very carefully.
Once all the pieces are removed from the window frame, clean out the recesses where the glass was set in the frame and any glazing compound and glazier points (those little metal pieces that help to hold the window glass in the frame) and any retaining strips (if there).
Now using a chisel and the mallet, scrape any residue or debris left from the recesses and carefully removing any debris without damaging the frame.
Once everything has been cleaned out, lightly sand the frame to get it smooth out any nicks caused from the scraping and apply a coat of primer or sealer.
In order to get a new piece of glass cut for the window frame, (measuring from the outside shoulders of the glass recess) measure the full width and height of the opening, subtract about a 1/8 inch from your measurements, and give that measurement to the glass shop to have your glass cut to fit the space. Do not forget to tell the shop the thickness of the original glass as well.
Now that you have the new piece of glass, carefully place it into the frame to double check that the fitting is correct. After you have confirmed the fitments, remove the glass and apply at the beat of caulking in the recess to create a bed for the new pane of glass to sit snugly. Gently push the glass pane into the fresh caulking to hold it while you get ready for the next step.
Now push the metal points (called Glaziers) using the putty knife or a flat head screwdriver into the wood frame about every 8 inches to hold the glass place.
Roll out the glazing compound into a 3/8 inch diameter and press it into the joints between the glass and the frame.
Create a flat even surface by holding a putty knife at a 45° angle, to smooth out the compound. Strip off any excess glazing compound and let the compound dry for several days before painting.