One dimensional nanowires systems with programmed multi-heterojunction along their axes have been presumed as an ideal nanomaterials platform for quantum confinements exhibiting novel electronic/photonic functions. Herein we have successfully produced free-standing nanowires with multi-heterojunctions of which spatial alignments are perfectly under control on a substrate by a facile protocol referred to as Single Particle Triggered Linear Polymerization method. Uniform nanowires were well-vertically aligned on substrates with tightly bound bases, and represented by the sequential bottom-up of ~ 10 nano-segments from copper phthalocyanine and Buckminster fullerene molecules. Efficient polymerization/crosslinking reactions with high enough G values of 20-40 (100 eV)^-1 were rationalize the formation of the nano-segments with significant changes in their radial thickness. Although the released energy density by the employed high energy charged particle was extremely high, which is presumed from the value of linear energy transfer of 1 – 1.4 ×10⁴ eV nm^-1, however electronic and Raman spectroscopies confirmed clearly that the nano-segments in nanowires reflected well opto-electronic characteristics of molecules at least the outer boundaries, suggesting the future application of the present multi-heterojunction systems as magneto-optical nanomaterials. We are able to make our own choices of the molecules with designed electronic states, and program them to 0-1 dimensional nanomaterials with sequential connection along a direction by the present technique.