Pre-raising the grain before applying a water-based dye or topcoat is a good way to deal with the fibers that pop up when you add water, but if you’re not careful, you could only press down the fibers you want to remove. My approach may sound unconventional, but it works. After finish-sanding and wiping the surface with a wet sponge, wait until the surface dries. Now using your final grit, very lightly sand across the grain.
Next, sand diagonally across the grain in one direction, and then in the other. This cross-grained sanding breaks away the fibers cleanly. Finish up
by sanding parallel to the grain, using similar pressure to erase any cross-grained scratches.