Wood Filler vs. Wood Putty

As perfect as you might make a match now, remember that the wood and the filler will age differently. When we moved into our house, I had a hard time finding how the cabinets were assembled - finally found well hidden nail holes. Now 15 years later the hidden nail holes stand out like a sore thumb.
 
Yep, I had done some sanding, and I opened up my vacuum bucket and took out some of the fine sanding dust, mixed in some titebond with a popsicle stick until it made a thick woody paste and spackled it right in. Worked like a champ.

I know you posted this a long time ago but do I do this before or after staining? In my mind I should do this first and then apply the stain and top coat.
 
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All here make great points and cases for their methods. Fillers before finish and puttys after finish. With finer works one should always endeavor to not use mechanical fasteners where they will be seen and require fill. This is not always possible but....
some methods I've found to be effective albeit unorthodox at times are for one as Mike mentioned the shellac sticks. They can be melted together to create matching colors. One way I use them is before I finish the piece. I will take a sample board of the same batch of wood I am using and apply the finish. Then make a match with the shellac stick and apply it to the defect or hole in the unfinished piece. Since it doesnt take a stain it blends well once the finish is applied If it is to hide a nail or Brad often times I will deform the hole so it is irregular in shape. Then fill and sand flush. Another way using the shellac sticks is to make the defect or hole appear as a piece of the grain. Which as the piece ages will not stand out.
epoxy tinted with Trans tint or other dyes is good for larger defects or to fill a knot.
If the piece is going to be finished with a solid color say paint or pigmented lacquer then I use formula 27 or bondo. Sanded flush it makes an invisible fix once the finish is applied.
waxes are good for on site touch ups or to fill in field applied parts such as the moldings as its the most efficient and easiest to apply in the field.
 
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