Make the burrow where you want them to go, then go into the military (m) screen, and then the alerts (a) screen, then you just highlight the burrow you want and hit enter, that tells all civilians to stay the hell inside that burrow.
EDIT CURSES!!!
Edit with a real post now, since something happened and I'm still the last person to have posted.
It was horrible. A massive puppy slaughter. Goblins ambushed my fortress, my military is only half prepared, wearing only iron breastplates and leather everywhere else. At least their weapons are adamantine.
But that isn't what causes the slaughter, my killing hall is only half done. My design is a 3 wide hallway with locked hatches flanking each side. My melee military opens those hatches and charges out of the ramped rooms underneath, slaughtering everything in the hallway, instantly going from out of sight to melee range in 1 move. But half of the hatches aren't built, and the military goes through the killing hall itself to get into their stations, instead of the access tunnels. The enemy is marksgoblins but enough of the hatches are in place to still protect the melees for an ambush.
Despite the inadvisable route, the military makes it into the channels on each side of the hall just before the marksgobs get in range. Unfortunately the war dog. The mother of every single dog in the fortress is assigned to the militia commander, and follows her master into the channel.
Her veritable hoard of puppies however, aren't so lucky. The goblins open fire, painting the white limestone walls and floors of 'Whitefortress' red with puppy blood. The goblins ACTUALLY RUN OUT OF AMMO and there are still puppies bleeding out in the hallway. In anger at the loss of so much
food innocent life. My military charges out of the hatches and turn the now defenseless goblins into kibble for the survivors.
The flying ({copper arrow}) strikes The Dog in the right front leg, tearing apart the muscle and bruising the bone!
A tendon has been torn!
The flying ({iron arrow}) strikes The Dog in the right front leg, shattering the bone!
A tendon has been torn!
The ({iron arrow}) has lodged firmly in the wound!
The Stray Puppy gives in to pain.
The Stray Puppy falls over.
The Dog gives in to pain.
The Dog falls over.
The flying ({iron arrow}) strikes The Dog in the right front leg, shattering the bone!
A tendon has been torn!
The ({iron arrow}) has lodged firmly in the wound!
Othurtak Tuoritheltuoritha, Carpenter cancels Store Item in Stockpile: Item inaccessible.
The flying ({copper arrow}) strikes The Dog in the upper body, tearing apart the muscle!
A tendon in the upper spine has been torn!
The ({copper arrow}) has lodged firmly in the wound!
The flying ({iron arrow}) strikes The Stray Puppy in the lower body, tearing apart the muscle and tearing apart the guts!
The Stray Puppy looks sick!
The Stray Puppy (Tame) has bled to death.
Othurtak Tuoritheltuoritha, Carpenter cancels Store Item in Stockpile: Item inaccessible.
The flying ({copper arrow}) strikes The Dog in the tail, tearing apart the muscle and bruising the bone!
An artery has been opened by the strike and a tendon has been torn!
The Stray Puppy regains consciousness.
The flying ({silver arrow}) strikes The Stray Puppy in the upper body, tearing apart the muscle!
A tendon in the upper spine has been torn!
The ({silver arrow}) has lodged firmly in the wound!
The flying ({iron arrow}) strikes The Stray Puppy in the right front leg, shattering the bone!
An artery has been opened by the strike, a sensory nerve has been severed and a tendon has been torn!
Kart Nesingyterux, Dog (Tame) has bled to death.
The flying ({copper arrow}) strikes The Stray Puppy in the left front leg, tearing apart the muscle and bruising the bone!
An artery has been opened by the strike and a tendon has been torn!
Othurtak Tuoritheltuoritha, Carpenter cancels Store Item in Stockpile: Item inaccessible.
Mrivim Maekghorn, Brewer cancels Store Item in Stockpile: Item inaccessible.
The flying ({iron arrow}) strikes The Stray Puppy in the left front leg, shattering the bone!
A motor nerve has been severed and a tendon has been torn!
The Stray Puppy (Tame) has bled to death.
I need to complete my hallways of goblin genocide earlier in the year...