Preparation is 90% of the finish. If you see the seam, then you didn't do a good enough job filling and sanding prior to painting.
Sometimes blending fillers can be difficult if they are harder or softer than the surrounding surface, as the filler will tend to sand at a different rate. Careful sanding with a long sanding block should help to get a smooth surface.
If you can feel any defects during the prep work, you'll definitely see them when paint is applied.