Hi Yen,
Here is a file I did, though I changed it up a bit. If the pipe dimensions dont work for what you want then I'll explain what I did.

The 2 pipes in your model are actually very slightly "Intersecting". THis is throwing a tiny little sliver into the mix where the 2 pipes meet and touch the building.

Also the to ends of both pipes just bairly touch each surface. These should "punch through" a bit to get a good boolean.

Hope that helps,
Burr

[EDIT] I posted a file that had an anomoly in the short pipe, I fixed it and replaced it here. If you got it fast please redownload this fixed version. [EDIT]