Generally waviness in sheeting is caused by not having enough formers or ribs in the structure. Long unsupported structure causes dips.
Another common cause is not using a sanding block.Using your hands will almost inevitably cause you to sand dips or waves into a structure.
This is not a candidate for fillers and there is nothing to catch the filler and give it a bonding surface. Glass will not fill it but will make it much more noticable so everyone will comment on your wavy fuse or wing.
Possible solutions more stringers in the fuse or half ribs in the wing. if possible use a harder balsa or thicker stock if your design can carry the weight.
For fuselages you also might consider strip planking if you can't add more stringers. Strong and light but more time then slapping a piece of wood on.
Hope that this is useful to you.
Dennis