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I assume you mean Lumerical MODE- FDE solver (or FDTD), you can simulate LC:Â
https://optics.ansys.com/hc/en-us/articles/360034915153-LC-Rotation-Simulation-object
FDTD examples  https://optics.ansys.com/hc/en-us/articles/360043705813-Liquid-crystals-list-of-examples
FDE is to solve eigen modes for waveguides. Make sure you have the proper waveguide cross section.
https://optics.ansys.com/hc/en-us/articles/360034917233-MODE-Finite-Difference-Eigenmode-FDE-solver-introduction
https://optics.ansys.com/hc/en-us/articles/360034396734-FDE-solver-analysis-Mode-List-and-Deck
https://optics.ansys.com/hc/en-us/articles/360034916973-FDE-solver-Simulation-object
https://optics.ansys.com/hc/en-us/articles/360034917333-FDE-solver-analysis-window-overview
https://optics.ansys.com/hc/en-us/articles/360034396914-Tips-for-finding-modes-in-FDE-and-the-mode-source
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I am not sure what do you mean "a mechanical alignment layer top of the liquid crystal."Â you can directly add a rectangle geometry with desired material on top of the LC object. If you want to add such a rectangle along the direction of the lc molecule, it should have one LC direction uniformly, ideally along the coordinate axis.
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