Techniques for managing data in a non-volatile memory system (e.g., Flash Memory) are disclosed. A controller can use information relating to a host's file system, which is stored by the host on non-volatile memory, to determine if one or more clusters (or sectors with clusters) are currently allocated. The controller can use the information relating to the host's file system to identify when the host is sending data to the next free cluster and to store such data in a sequential format by copying data from other locations in the non-volatile memory.