In future should this arise, it is helpful to grab your phone or similar and take a photo of what you are dealing with and post it here to let others know what you are dealing with. It would help to know what OS engine you are talking about and if the muffler is still attached. Some mufflers attach with the screws entering the engine from the muffler side (they go through the muffler and into the engine. Others go through the engine and then into the muffler.
Obviously if it is the prior then one screw will be next to impossible to get at with a drill or any other implement as the muffler gets in the way. If it is the latter then a different techniques are called for. For both the path of least resistance (If the muffler is still attached) is to get rid of the screw heads. If it is the type where the screws pass through the muffler lugs and screw into the engine, Taking a file or other method to remove the screw heads, allows you to remove the muffler and you are left with about a quarter inch of screw sticking out of the engine to grab with vice grips and carefully wiggle the free.
If it is the type that pass though the engine first then screw into the muffler, knocking the head off lets you remove the muffler and you have the remainder if the screws sticking out of the muffler. As these screws are relatively small either using a drill or a file to remove the heads is the path of least resistance. Actually this is usually the best approach for getting small screws out of just about anything.