Loosen the nails attaching the spindle to the handrail and runner using a hammer or chisel. Loosen the return at one end of the staircase to remove the spindle, if necessary. Wiggle the individual rail around until you can slide it loose. Repeat this step with any spindles you're replacing.
Take the spindles to a turner or staircase builder to replicate them, so you'll get a proper fit.
Clean and sand the area around the missing spindles, especially the threads where they fit into the handrail and baseboard.
Sand and paint your new spindles the desired finish.
Measure the distance from the handrail to the baseboard so you know how tall to cut your new spindles. Use a bevel gauge to determine the angle of slope to cut on the top. Cut the top of the spindle using your measurements.
Set the first rail into the bottom thread, and then the top, checking the fit. Glue the spindle into the threaded area at the baseboard and under the handrail. Secure with 2-inch hardwood trim nails at both the top and bottom, using about two to three nails each.
Find the handrail's support brackets. They typically sit at the top, middle and bottom of the banister and are attached to the wall. Remove the screws and brackets from the top and bottom of the staircase, and remove the middle bracket last.
Tap a finished nail into the previous screw holes to ensure the brackets were attached to a stud. Mark and drill new holes next to the old ones.
Fill the old screw holes with putty, and scrape off the excess compound.
Screw the new bracket on the bottom of the staircase to the wall, using the holes you've drilled. Repeat this step with the top bracket.
Attach the handrail to the top and bottom brackets per manufacturer directions, screwing into the bracket holes.
Install the center bracket into the wall, and attach it to the rail.