The quick and (dirty way) :
Right click on a target folder
(s)
Go to folder(s) properties,
Mark folder as Derived
like that.
Derived entities are excluded from searching by default like that.
The (safe way) :
By create a working set
That include only those entities you want searched and search only within that working set.
In our case will include ALL without target folder
(s).
Note : This answer is related to
Exclude folders from Eclipse search