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We go through similar with my 2.5 year old but we've mostly nipped it in the bud.
If he eats all or most of his dinner in an appropriate amount of time he gets a reward (piece of chocolate). If he doesn't eat "enough" dinner he is not allowed to eat anything else that night. He eats breakfast when he wakes up.

Our son is a skinny boy too, but he eats a ton throughout the day and he needs a little tough love now and then.
We find it helps giving him choices for dinner (ie would you prefer chicken or sausages, potatoes or carrots)

@irene: We are doing this right now with N. The doctor recommended like pp said to simply offer what he didn't finish at his meal and no other choices. It works most often. We are breaking bad habits started by Papa. N is pretty small for his age so I worried but the doctor said as long as he isn't losing weight then we could stick it out.

Has your doctor expressed concern about his height or weight? Or do you just feel like he looks small compared to his peers?

What do you give him when he says he's hungry? DD pulls this sometimes and I'll ask her what she wants. When she can't say, sometimes I'll say "2 pistachios" and she'll say yes, eat 2, and then go to bed. So I know them that she's not really hungry. We do let her eat raisins during books before bed.

I would probably make a bedtime snack part of your routine. My lo is very small so I have issues limiting food, but he eats ok at meals (not always). There have been nights where he has chicken as a snack before bed... If it's a routine, he's getting what he needs and dinner is totally separate issue.

We mostly use the "Division of Responsibility in Feeding" and it's worked really well (though we could just have a naturally good eater, who knows). It completely took away the power struggle around eating. http://ellynsatterinstitute.org/dor/divisionofresponsibilityinfeeding.php

We also do milk before bedtime so at least we're guaranteed some fat/calories then. If your ped isn't concerned about growth, I wouldn't worry too much about it.

Ideally (and this def doesn't happen for every meal), we serve family style so put a few different options in the middle and then we each serve ourselves. We help him, but basically he chooses what he wants from the options we've laid out, so there's not too much waste. He can ask for more of whatever he wants until it's gone - for example, if we're having fajitas, he may just want a tortilla with guacamole and shredded cheese, and we don't pressure him to add veggies/chicken. Basically we try not to put the hard sell on any particular food and treat it all as equal, model good eating, and keep meal time fun and relaxed. So far it's worked out well and he has, in fact, started eating the healthier stuff of his own volition. Some days he'll barely eat anything but then the next day he'll be ravenous - it seems to even out. He is skinny, but we were skinny kids too so I think it's just in his genes.

A few things that have helped us.

1) A divided childs plate. She can scoop and eat easier.
2) Only putting the 3-4 bites we want her to eat on her plate. Don't load it up. Let her get the satisfaction of finishing a section.
3) Leave the plate sit out for maybe another hour (dinner ta 6-630 and reoffer at 7-730 before tossing it). After that no more stacks. We find even an hour later she may be hungry
4) Healthy snacks are ones mom and dad get to pick. We don really stress too much if she calls it a snack or a meal. There are times she has gotten cold slices of chicken from the fridge, or we've heated up some frozen broccoli. If they are hungry they should eat whatever.

How does your LO eat at school? My LO is some times picky at home but peer pressure is a beautiful thing and she eats everything at school so I don't stress if she doesn't eat perfectly at home. I would definitely stop forcing him to finish everything on his plate, it just creates a negative association with food, and will eventually stop him from being able to know when he's full. As others have suggested, I would just save any left over dinner and continue to offer it as the only option any time he says he's hungry later in the evening.