The best exercise I've ever done is a plotting exercise. It helped me write a couple of strong plots with little to no filler. I was encouraged to write out my entire story in short sentences using BUT and THEREFORE. Doing this makes sure that there's a causal link between each scene (or even each action, as in the example below) in your book.

For example...
Dean was going to be late for dinner,
Therefore he took a shortcut through Farmer Jackson's field
But Farmer Jackson's prize bull was in the field and started chasing Dean,
Therefore Dean ran,
But the bull ran faster
Therefore Dean realised it was fruitless to flee
Therefore he looked around for a weapon...


Of course, there will always be times when something happens that isn't directly caused by anything in your book (e.g. if your inciting incident is a meteor strike, your protagonist may have had nothing to do with causing that). In my experience, as long as you can connect most of the major happenings in this way, that's a good way to ensure your story isn't full of unnecessary padding.