it has come time to call the exterminator and have our house treated. will the chemicals used have a negative effect on the fish? if so how can i protect them?

Yes, they may. I would advise placing a sheet or something like that over they're aquarium for the duration of the extermination (hey that ryhmes ) and maybe a bit after.

in the building that i am managing, we used to have the regular
pest control treatment. what i usually do is cover my tank with
the blanket and remove it three days later. i just lift one side
during feeding. the logic there: affected insect might drop dead
inside the tank, and fish who gonna take it will die too. we already
have that case for an arrowana tank inside an office.

yes i totally agree to what paul says... i did the same when i had it in my house...

gracias. will do

Like paul said, its not only the chemicals that can kill the fish, but the insects as well, due to them picking up the chemical and then getting into the tank.
your best bet is to totally cover the top of the tank for 3-4 days, and only move when feeding.