The semiconductor industry has continually sought the approaches to produce memory devices with increased memory cells per memory die. One way to meet the increasing storage capacity demand and reduce bit cost of NAND flash memories is 3D stacked flash cell array. In constructing 3D NAND flash memories, increasing the number of stacked layers to build more memory cell number per unit area necessitates many high-aspect-ratio etching processes accordingly the incorporation of thick and unique etching hard-mask scheme has been indispensable. However, the ever increasingly thick requirement on etching hard-mask has made the hard-mask film stress control extremely important for maintaining good process qualities. The residual film stress alters the wafer shape consequently several process impacts have been readily observed across wafer, such as wafer chucking error on scanner, film peeling, materials coating and baking defects, critical dimension (CD) non-uniformity and overlay degradation. This work investigates the overlay and residual order performance indicator (ROPI) degradation coupling with increasingly thick advanced patterning film (APF) etching hard-mask. Various APF films deposited by plasma enhanced chemical vapor deposition (PECVD) method under different deposition temperatures, chemicals combinations, radio frequency powers and chamber pressures were carried out. And -342MPa to +80MPa film stress with different film thicknesses were generated for the overlay performance study. The results revealed the overlay degradation doesn’t directly correlate with convex or concave wafer shapes but the magnitude of residual APF film stress, while increasing the APF thickness will worsen the overlay performance and ROPI strongly. High-stress APF film was also observed to enhance the scanner chucking difference and lead to more serious wafer to wafer overlay variation. To reduce the overlay degradation from ever increasingly thick APF etching hard-mask, optimizing the film stress of APF is the most effective way and high order overlay compensation is also helpful.