For decades high voltage alternating current (HVAC) was considered as most economical solution to transmit and deliver electric power. With the recent developments in power electronic devices, high voltage direct current (HVDC) system becomes most prominent technology. Multi-terminal direct current (MTDC) based system as a promising technology for future power system is the major focus area for researchers and industries these days. A number of MTDC systems have been implemented physically. The major motivation to construct such MTDC systems is the integration of large-scale offshore power sources such as wind turbines and solar systems. This paper discusses the most critical challenges and issues related to operation, control and protection schemes for integration of modular multi-level converter (MMC) based MTDC systems. At first detailed literature survey has been presented to show the challenges for MMC based MTDC systems, then an analysis related to those challenges for operation, control and protection schemes for existing MMC based MTDC systems has been provided. Finally, a road map to tackle such challenges has been suggested.