I think this answer is very difficult to give accurately. We're all different and digest foods in our own unique way, from the way we eat, the speed we eat at and the way our organs deal with the food. For a scientific answer you'd need to go to a specialist clinic. At a guess, I'd say between 60-75%.
If you're energetic the majority of that will go to keep cells and blood and organs going, and you'll burn most of them through physical activity /building muscle. If you're less active some calories will be stored as fat on a pro rata basis!!
The healthier you are the more you'll digest? That's a tricky one to answer....
It also depends on the type of food you eat. Fiber is taken in but only partly digested. It helps in absorption and with waste removal, so, as others have pointed out, eat plenty of fiber for better digestion.
If you ate 400 calories worth of raw food for example I'd guess that you'd digest a lower pecentage than if that same food was cooked?