Microgrids are the solution to the growing demand for energy in the recent times. It has the potential to improve local reliability, reduce cost and increase penetration rates for distributed renewable energy generation. Inclusion of Renewable Energy Systems(RES) which have become the topic of discussion in the recent times due to acute energy crisis, causes the power flow in the microgrid to be bi-directional in nature. The presence of the RES in the microgrid system causes the grid to be reconfigurable. This reconfiguration might also occur due to load or utility grid connection and disconnection. Thus conventional protection strategies are not applicable to micro-grids and is hence challenging for engineers to protect the grid in a fault condition. In this paper various Minimum Spanning Tree(MST) algorithms are applied in microgrids to identify the active nodes of the current topology of the network in a heuristic approach and thereby generating a tree from the given network so that minimum number of nodes have to be disconnected from the network during fault clearance. In the paper we have chosen the IEEE-39 and IEEE-69 bus networks as our sample test systems.