This paper investigates the properties of Copper-Selenium heterojunction nanowires before and after implantation. Heterojunction between Cu and Se was formed using the template method, assisted by chronoamperometry technique. Implantation in heterojunction nanowires was performed with 80 MeV Ni6+ ions for different fluencies ranging from 1x10(11) to 1x10(13) ions/cm(2). XRD studies show that no peak shifting takes place after implantation, but a significant variation in peak intensity was observed. Plane orientation and increased crystal quality may be the probable cause for variation in plane intensity. UV-Visible study for optical behavior shows a red shift in the absorption edge along with a decrease in the optical band gap. I-V measurements before and after implantation revealed an increase in the rectification behavior of Schottky junction, which may be due to the interface smoothing and a decrease in junction barrier height during implantation.