You can't keep mollies and guppies in distilled water. They will struggle for a few months and die. They need minerals.
You could mix distilled or reverse osmosis water with your tap water (50/50 mix). But you really need to find out what the GH (general hardness), KH (carbonate hardness) and pH of your water supply is. This information can usually be obtained from your water supply company's website or by telephoning them. If they can't help you, take a glass full of tap water to the local pet shop and get them to test it for you. Write the results down (in numbers) when they do the tests. And ask them what the results are in (eg: ppm, dGH, or something else).
Knowing the actual numbers for GH, KH and pH would help.
---------------------
To screen out microbes from water, you need very fine filters that contain micron screens or some sort of material that can trap bacteria, viruses, fungus, etc. These can be expensive to buy and difficult to find. Normally water companies add chlorine or chloramine to the water to kill these organisms.
---------------------
Some companies do big water filters and this might be easier because they hold more filtered water.