Embodiments of mechanisms for flattening a packaged structure are provided. The mechanisms involve a flattening apparatus and the utilization of protection layer(s) between the packaged structure and the surface(s) of the flattening apparatus. The protection layer(s) is made of a soft and non-sticking material to allow protecting exposed fragile elements of the packaged structure and easy separation after processing. The embodiments of flattening process involve flattening the warped packaged structure by pressure under elevated processing temperature. Processing under elevated temperature allows the package structure to be flattened within a reasonable processing time.