Filler is ok until the car gets bumped, it just is not stong in impact. So if you want to have handles again, you only need to hit it in the right spot and then you can put the handles right back in the holes.

There are ways of making the filler stay put:

1.best: welding a patch over the hole. Complete the work with body filler.

2. almost as good: Rivit a patch over the hole and finish with filler. Riviting is easier, takes less equipment and heat can burn paint or distort sheet metal.

3. less good: tack weld one or two lengths of welding rod across the low spot and then use filler. The filler will be locked in place but can still crack slightly at the edges.

4. you could run small screws into the depression to give the filler something to cling to, but they can't stick up much or it will be a disaster.

5 alternatively, you can drill a couple holes through the dimple for the filler to flow through and secure itself. Has the advantage in shallow depressions as holes can't stick up through the filler ruining the job