Delete some areas of the world

In our game, there are some areas which are static obstacles, like trees, walls, big stones etc. Characters can never move into these areas. While generating the RecastGraph, these areas are still included in the final result(with different area IDs).
How can I remove those areas from the final generated graph?

The dark red area is the walkable area what I want to keep in the final graph. All other areas are useless.

I’m sorry to bothering you. I just realized that I made a mistake: I use a big plane as the basic ground. so all the world are included in the Recast graph. I asked our artist to give me a basic ground with holes to generate the navigation mesh. It only contains the areas walkable now.
Is there any other way to remove those areas without change the ground mesh?

There is no easy way to remove them at the moment. I assume you want it for memory optimizations (it won’t do much for performance). But to get the optimal performance a few slightly complicated methods would have to be written.
I will move this to the feature requests category.