A main component of the Multi-Layer Multi-domain (MLMD) orchestration is the end-to-end path computation over the packet and optical layers. Routing in MLMD networks is complex and requires special computational elements and cooperation between different layers and domains. The goal is to optimize the utilization of Wide Area Networks (WANs) leveraging on FlexE - the new Flexible Ethernet technology which couldn’t be fully achieved from local resource allocation in a single domain. We present MLMD-PCE, a path computation engine for MLMD networks that achieves optimal routes through a hierarchical path computation. We formulate an optimization problem of traffic routing and resource assignment for FlexEAware and FlexE-Unaware modes and propose an approximation algorithm that runs in polynomial time. Another issue of multidomain routing is the lack of visibility over the intra-domain typologies in the parent-PCE. To solve this problem, we use a novel mechanism to gather the intra-domain information from the child-PCEs while keeping the domain privacy. Simulation results show that MLMD-PCE carries 77% more traffic than the current Hierarchical-PCE.