Electronics, in particular VLSI technology, has made possible design of sophisticated, complex and powerful systems for user. Although silicon technology is evolving continuously to produce smaller, faster and reliable systems with low power, eventually the integration of Microelectronics and Photonics with Nano-chemistry as the driving force is the new area of research that spans from environmental management , smart health-care, smart energy management to new innovations in communications, processing and man-machine interfaces. This has created tremendous opportunities for realization of new systems. The co-existence of silicon technology with these emerging technologies, photonics and nano-chemistry has created new design opportunities for the designer, bringing new challenges to be solved. In this paper, some of the important challenges have been discussed.