A method to fabricate a carbon nanotube (CNT)-based transistor includes providing a substrate having a CNT disposed over a surface; forming a protective electrically insulating layer over the CNT and forming a first multi-layer resist stack (MLRS) over the protective electrically insulating layer. The first MLRS includes a bottom layer, an intermediate layer and a top layer of resist. The method further includes patterning and selectively removing a portion of the first MLRS to define an opening for a gate stack while leaving the bottom layer; selectively removing a portion of the protective electrically insulating layer within the opening to expose a first portion of the CNT; forming the gate stack within the opening and upon the exposed first portion of the carbon nanotube, followed by formation of source and drain contacts also in accordance with the inventive method so as to expose second and third portions of the CNT.