The design specification of CubeSat standards by California Polytechnique University has become a major milestone in development and deployment of nano satellites. The number of CubeSats that are being deployed into the orbit has increased in recent years. The design and development have been transformed from traditional hardware devices to software defined radios. However there is a lack of clear understanding and concrete findings on developing proper communication transceivers. The lack of knowledge of proper guidelines to be followed to design and develop communication subsystems prompts and acts as a base for us in understanding the communication subsystem design standards followed by CubeSat projects in various universities. Particular attention is given to those CubeSats that are currently in the orbit and are under development. The main aim of the thesis is to identify the challenges faced by the CubeSat developers and provide guidelines for future developers in order to overcome those challenges to reduce the development time and costs which are major constraints in CubeSat developments. A traditional literature review process was followed in order to identify the potential issues and in parallel a modem was designed and implemented in order to know some more challenges while developing a CubeSat modem. From the literature review method, eight potential issues were identified and an additional two more challenges were experienced while implementing a modem. Potential advantages and disadvantages of using nanoRTU have also been identified as part of the work.