Is this an engine that currently runs? By that I mean are you trying to check the timing or are you trying to complete a repair such as changing the timing belts?
If the engine you're working on currently runs and you can't see the timing marks, your light is probably not hooked up to the number one plug (like Mr. Loyale had mentioned) make sure the light is firing from the #1 sparkplug or else you probably won't see the timing marks.
If you just changed the timing belts and are verifying the camshafts are correctly timed to the crankshaft, those are a completely different set of marks yet still on the flywheel.
Also, like Mr. Loyale mentioned, the timing marks are on the flywheel, so if you are pointing the gun at the harmonic balancer -- which is typical for many makes but NOT Subaru, you will never see the marks until you are looking for them on the flywheel -- which means removing the rubber plug where the tranny/engine marriage takes place