"My level contain mdl s and hmp terrain. All work fine. When i create simple box with invisible flag(for creating unpassble areas). I see error Message CRITICAL ERROR E003 - no
visible blocks in map."

This means there is no level geometery visible. In order to do what i think you want to do, you can simply make a small cube with no flags set, (default visible) and hide it way under the level and terrain so you cant see it anyways.