I use a different method to Swanny, you will need to decide which works best for you.
Materials:
Tube putty
Thinner
Rag
Toothpick
I mix some of the tube putty(Tamiya or Gunze in my case) with the thinner to get it into a pasty consistency.
Apply over and into the seam.
Next take a rag soaked with thinner and run it over the seam removing any excess, avoiding of course removing putty from the seam.
Pick out your putty paste from detail while still soft.
Let dry and sand down if needed.
Process can be repeated if needed.
There is another method I use but I think it might give a few guys gray hairs, as it involves removing ALL the alignment pins.