I am trying to bake a Cycles material to a texture, but I keep getting this unwanted black line where to two different materials meet, anyone know how I can fix this?
You don’t really show the material nodes but are you using the corrects UVs to apply the texture to your model.
Please supply demo blend file and texture for further review
The subsurf modifier is creating this. Did you unwrap and take into account the change in the shape of the mesh with this modifier added (option in uv unwrap settings)
One option, select the vertices and remove doubles (W / remove doubles)
