A memory system comprises a flash memory and a controller comprising a control logic circuit and a working memory storing a flash translation layer. The memory system performs a merge operation by selectively copying a page from a first block of the flash memory to a second block of the flash memory. Where the page is valid and marked as allocated according to a file allocation table stored in the flash memory, the page is copied to the second block. However, where the page is valid and marked as deleted in the file allocation table, the page is not copied to the second block.