That's a common problem. In some cases it can be fixed before assembly by sanding one edge of the joint so they will line up properly. Sometimes it's caused by something as simple as a piece of flash that you didn't notice. If the entire piece is too high, put a piece of sandpaper on a hard, flat surface and sand the edges of the whole part. The hard surface will make sure all edges are sanded evenly. Rotate the part in our hand while sanding since you will unciociously put more pressure on one side than the other.
I usually try to fix problems like that by sanding the high side down. If there are sunken rivets or panel lines in the area that will be sanded I usually make them deeper before I start sanding so they will still be visible when I'm done.
Squadron putty will work, but if there are panel lines to be rescribed that is difficult to do across putty since it just flakes out.
If there is a major difference between the two pieces, regardless of how you do it, your feather distance will have to be significant or the joint will still be noticeable.