If you have an assembly that you have imported, is one of the parts in the assembly grounded? If so, you can unground it and constrain it to the origin planes to get it aligned with the global coordinate system. Once it is aligned you can reground the part and remove the constraints.
If it is just a part (somebody correct me if I am wrong) then you will need to try and straighten it out in MDT and reinport it.
Also, if it is a subassembly in a larger assembly, constrain it to the existing assembly to get both of the coordinate systems aligned.