This paper proposes a novel application-specific hybrid coarse-grained reconfigurable architecture with a flexible network on chip (NoC) mechanism. Architecture supports variable block size motion estimation (VBSME) with much less resources than ASIC based and coarse grained reconfigurable architectures. The intelligent NoC router supports full search motion estimation algorithm as well as other fast search algorithms like diamond, hexagon, big hexagon and spiral. Our model is a hierarchical hybrid processing element based 2D architecture which supports reuse of reference frame blocks between the processing elements through NoC routers. This reduces the transactions from/to the main memory. Proposed architecture is designed with Verilog-HDL description and synthesized by 90 nm CMOS standard cell library. Results show that our architecture reduces the gate count by 7x compared to its ASIC counterpart that only supports full search method. Moreover, the proposed architecture operates at a frequency comparable to ASIC based implementation to sustain 30fps. Our approach is based on a simple design which utilizes a high-level of parallelism with an intensive data reuse. Therefore, proposed architecture supports run-time reconfiguration for any block size and for any search pattern depending on the application requirement.