An apparatus of a memory system and an operating method thereof include: a plurality of memory devices, wherein each of the plurality of memory devices includes a plurality of blocks, each of the plurality of blocks has multiple pages corresponding to multiple wordlines, respectively; and a memory controller coupled with the plurality of memory devices, wherein the memory controller is configured to determine an overhead of an erase block where a deleted file resides therein, perform file level secure erase operation on the erase block in accordance with at least the overhead, and mark target pages corresponding to the deleted file as “trimmed” in a logic block address (LBA) table.