Translation:You run through the building and jump out the window.
As Ryagon IV says, to run across the building suggests the outside, but if it was run across the room/ floor/ etc, it would be possible. I think it's because "building" has a 3D idea to it, which works with "through", but "across" is more suited to movement across a planar surface.
I got burned with "You run over to the building and jump out the window". I came back to this exercise because the module cracked. This is the first time I have seen át- as "through"; I have it down as "across" or "over". There seems to be too many of these odd combinations to cover in the Preverbs area.
Átfutsz az épületen.
Át- = across, through, over (direction?)
-en = in (location?)
(You run across)(the)(in building) = Meh, it makes sense.
When you're moving through something, from one side to the other, that medium you're moving through will receive the '-on' suffix. If you used épületben, it would be some movement from one place to another within the building.
- át az épületen - through the building
- át az épületben - in the building
Oh, if you know German, it's a bit easier. The general meaning of the prefix át- translates to "hinüber-" or "herüber-" or generally "über". Von der einen auf die andere Seite.
Átülsz a másik székre? - Setzt du dich hinüber auf den anderen Stuhl?
A híd a folyón vezet át. - Die Brücke führt über den Fluss.
It just breaks down a bit when you're talking about moving through some specific space, like in the building sentence. Then you have to do with "durch":
Átfutunk az épületen. - Wir rennen durch das Gebäude.
Átfutunk az épületben. - Wir rennen im Gebäude hinüber (z.B. in einen anderen Raum).