The hybrid integration of silicon metasurfaces, in forms of insertable thin-film elements, into a multilayer polymer waveguide platform is introduced. Owing to the wavelength comparable thickness and high efficiency of the dielectric metasurfaces, the designed devices can manipulate beams in a relatively short distance with low insertion loss. They can also realize functions critical for three-dimensional (3D) photonic integrated circuits (PICs) that are difficult for conventional micro-optic elements. The designs of several key photonic components are presented in this work as proof-of-concept. Specifically, three applications based on the proposed platform are demonstrated numerically, including on-chip beam collimation, spatial mode (de)multiplexing, and focusing vertical out-coupling. These functionalities can be realized within a short propagating length. This work presents a theoretical study on the design principles and performances of the proposed devices, which can be implemented by adopting the existed technology of inserting classic thin-film elements into photonic chips in the near future. The results suggest a novel and general path for optical signal manipulations within the 3D photonic chips and may prove useful in the design of transceiver devices for optical communication, optical sensor chips, compact chips for optical computation, etc.