One subject that I often get asked about is how to deal with filling nail holes on stained woodworking projects. The problem is generally two-fold:
-Wood fillers typically don't take stain as well as the surrounding wood
-Wood fillers placed on unfinished wood that are allowed to dry and then sanded flush will often cause the area surrounding the filled hole to appear discolored after the finish is applied.
There are a number of techniques for dealing with these problems, and what works on one project may not necessarily work well on another. However, by testing on scrap stock, you should be able to find a solution that will fit the needs of your woodworking plans.
The first one we'll discuss is for softwoods such as pine, fir, maple and birch. When you intend to stain such woods, I'd highly recommend using a pre-stain conditioner to help even out the color of the stain. Applying a pre-stain conditioner before filling the nail holes would address the problem of the wood filler affecting the surrounding wood, as it would help prevent the filler from penetrating the surrounding stock. Keep in mind that the manufacturers of such products typically recommend applying your stain within two hours of the conditioner's application, so after filling your holes and allowing the filler to dry, you may have exceeded the two hour time period.
In that event, simply apply a second coat of conditioner before staining. Also, be careful when sanding your filler so as to avoid sanding the conditioned wood around the filler.
Another solution, of course, would be to apply the wood filler before you begin the sanding steps of your woodworking plans.
As a result, the filler and surrounding wood will be sanded at the same time, thus minimizing the effect on the stock surrounding the filled hole when stain is applied.
If your problem is that your filler of choice doesn't match your stain color well, you can try some other ideas. One of the most common is to use a powder-style wood filler mixed with the color stain you wish to use. This technique can be used whether you choose to fill the holes before or after staining the wood, but if you choose to stain before filling, take care when sanding the excess filler to avoid damaging the surrounding stock.