A method for patterning CNTs on a wafer wherein a CNT layer is provided on a substrate, a hard mask film is deposited on the CNT layer, a BARC layer (optional) is coated on the hard mask film, and a resist is patterned on the BARC layer (or directly on the hard mask film if the BARC layer is not included). Then, the resist pattern is effectively transferred to the hard mask film by etching the BARC layer (if provided) and etching partly into, but not entirely through, the hard mask film (i.e., etching is stopped before reaching the CNT layer) Then, the resist and the BARC layer (if provided) is stripped, and the hard mask pattern is effectively transferred to the CNTs by etching away (preferably by using Cl, F plasma) the portions of the hard mask which have been already partially etched away.