If you filter it, you could pour it back into your tank.
If the fuel was growing bugs inside your tank, then you haven't fixed the problem by just draining the fuel. The bugs (it's not algae, but bacteria... bugs!) are still in your tank, laying on the bottom and sides... everywhere. You'll need to shock it with an anti-microbial additive like Biobor or similar.
The bugs don't actually grow in the fuel, but in the boundary layer between the fuel and moisture that has accumulated in the storage vessel (tank, storage container, etc). So, if you keep your fuel dry, you won't have a problem with bugs. Unfortunately, easier said than done at times.
Since the bugs don't actually grow in the fuel, but in the boundary between the fuel and moisture (water) that has collected in the fuel, you could filter it and then return it to the tank along with a shock treatment of anti-microbial additive to kill the bugs growing in your tank.