If the treants don't leave, it sounds like a great challenge. Quit wasting bolts on them, and instead hunker down under the earth, training and forging, until you're ready to burst out on the treants with seasoned soldiers and quality equipment. Axes, I'm thinking.
If they're the Relentless Assault treants, you actually want hammers, since they have no internal organs and [SEVERONBREAKS].
Also, they don't have [trAPAVOID]. You may be better off building loads of weapon traps full of the wooden maces you've picked up from earlier sieges.
Following the above, "if it is Relentless Assault Treants"
Pardon me, but first: yes, the siege will end on its own eventually, but no, you don't want to use hammers on them. In fact, you don't want to try to melee them at all. It doesn't matter how many limbs you break, because they don't bleed, feel pain, become stunned, knocked unconscious, or nauseated. Shooting them with projectiles is indeed the only reasonable way to get rid of them. Without resorting to traps.
For an illustration: I sent 3 champions in full steel (from + to * in quality, all we had) at a very small squad that was trapped and trying to escape after a siege. This is in Sparkgear, mind you. The champions severed some limbs, which didn't even slow the treants down. Then they lost their weapons, and were left wrestling with them for
almost two months, during which time they all became tired/overexerted, thirsty, and two eventually took serious wounds. After about a month of them deadlocked with the unharmable trees (remember these were also legendary wrestlers), I sent in 8 near-lordly hammerdwarves. They manged to kill a couple of treants in exchange for multiple wounds and one death. Still left with about 4 treants, and trapped/wounded/thirsty champions still wrestling alongside trapped/wounded hammerdwarves, all tired and unable to do much harm to the treants. I sent in 3 marksdwarves, one an elite, and the battle was over in about 2 game days.
Projectiles. Because [SIZE] doesn't matter to an *Iron Bolt*. It does however prevent dwarves without at least mastercrafted steel or base level adamantine weapons from dispatching creatures properly.
Edit: typo