The primary improvement is to ensure all internal surfaces of the manifold are smooth as it increases gas flow and discourages the build up of carbon deposits, which restrict flow.
This can be done by grinding out rough areas where casting slag/sand is imbedded in the runners or where there are sharp edges. Furthermore grinding of the material should ensure that the manifold runners match the exhaust ports of the cylinder head. For this a manifold gasket can be trimmed to the cylinder head, and then the gasket can be used as a template to grind the exhaust manifold.
In some cases there are exhaust manifolds consisting of two or three piece items, bolted together. It should be assured that the flow is optimal at each join.
Due to the shape and bends of the exhaust manifold, there will be areas that cannot be grinded, which leaves you with two options:
Extrude honing should be done carefully as overenthusiastic usage can grind the material thin, which can result in cracking from heat or vibration.
The outside of the manifold should also be checked, removing off all sharp edges left over from the casting process. This allows a more uniform spread of heat and cool down providing less stress points.
As a final point, some manufacturers cast all port runners in a single piece, due to the simplicity of production. Unfortunately this stresses the manifold as it heats and cools down, which can create fractures at the runner/flange joins or break the manifold studs. A simple fix to this is to cut the flange so each runner’s flange is separate from the other runners’ flanges. Cuts should not be made if stud holes are placed inappropriately, as it will result in leaks, due to uneven clamping. If done propery, it will also improves the seal, minimizing leakage from the manifold gasket. An example of this in the right image of a BMW M52 exhaust flange, where the red lines outline where to cut the flange to separate the runners.