I am using a Pre-Populated SQLite Database with Core Data.
My problem is that i want to encrypt sqlite database file generated by Core Data
Apple includes support for its CommonCrypto library in iOS, and has a sample code project to demonstrate use of asymmetric and symmetric encryption/decryption.
Which approach you take depends on how you intend to secure the data; a symmetric approach could require storing the key in the application, which reduces security somewhat. But the sample code should get you started, either way.