An alignment data structure is used to map a logical data block start address to a physical data block start address dynamically, to service a client data access request. A separate alignment data structure can be provided for each data object managed by the storage system. Each such alignment data structure can be stored in, or referenced by a pointer in, the inode of the corresponding data object. A consequence of the mapping is that certain physical storage medium regions are not mapped to any logical data blocks. These unmapped regions may be visible only to the file system layer and layers that reside between the file system layer and the mass storage subsystem. They can be used, if desired, to store system information, i.e., information that is not visible to any storage client.