Once you have put screws into dressed timber (dressed timber is smooth finished timber that is best stained or vanished) you are left with the ugly head of the screw showing. How do you get the natural lines of the timber back? You can use colour matched timber putty, but to be honest, timber putty always looks like timber putty. The best alternative is timber plugs. What are timber plugs? Timber plugs are cylinders of timber (as shown in the picture) cut out of timber using a plug cutter (a type of drill bit).
When you cut your dressed timber, keep a piece of the off cut to use for cutting your plugs out of (what I do is keep an off cut of every piece of dressed timber, so this way I can match the timber plug exactly with each piece of timber). When you install your dressed timber you need to get a spade bit (a type of drill bit) that is the same size as your plug cutter. This is so you can counter sink the head of the screws by 4-6mm using that spade bit, that when you install your plugs they will fit nice and tight in the counter sunk screw hole. Glue in your plugs insuring that the glue goes around all the edges of timber plug and the timber grain on the plug follows the same direction as the grain on the dressed timber. Once the glue has tried come back and with a sharp chisel, cut the top of the plug off, leaving it about 0.5mm high. From here get some sand paper and sand the remainder of the timber plug flush with the dressed timber. Now you are ready to vanish/stain your timber.
Using timber plugs takes a little more time to do than using timber putty. The difference between timber plugs and timber putty is massive, and will make all the difference in making your deck look a million dollars.