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1. You can prepare the finite element model for other engines like ansys and nastran and pro mechanica will not be used in these case. Your finite element model shall be opened in ansys or nastran then u can run solver in those program following by post processer in that program only.--For these use analysis FEM mode. Ask me if you need any further help on these issue.
2. Heat transfer can be calculated there has option to set heat transfar coefficients for conduction/convection/radiations. However as per your requirement you may need to carryout certain idealisation with you model.