The subcube allocation problem in faulty hypercubes is studied in this paper. An efficient method for forming the set of regular subcubes is proposed. A concept of irregular subcubes is then introduced to take advantage of the advanced switching techniques such as wormhole routing to increase the size of available sub cubes. In this paper, a two-phase fault tolerant subcube allocation strategy is proposed. The first phase is the re configuration process based on a modified subcube parti tioning technique which finds the set of disjoint subcubes in the faulty hypercube. The second phase is to apply an existing fault-free subcube allocation strategy such as Buddy strategy to each disjoint subcube for assigning the fault-free available subcubes to the incoming tasks. The simulation results using Buddy strategy are also given.