A system and method for logically organizing compressed data. In one aspect, a destination storage server receives a write request that includes multiple data blocks and specifies corresponding file block numbers. An extent-based file system executing on the storage server accesses intermediate block entries that each associates one of the file block numbers with a respective extent block number. The file system, in cooperation with a compression engine, compresses the data blocks into a set of one or more compressed data blocks. The file system stores the compressed data blocks at physical locations corresponding to physical block numbers and allocates, within an extent map, pointers from an extent ID to the extent block numbers, and pointers from the extent ID to the physical block numbers.