Dear Victor, you, my friend, have quite an imagination!
Bacteria and viruses are typically much smaller than mammalian cells. Typical bacteria would be less than 1 micrometer (um) in diameter. hence, we use 0.22 micrometer filters to screen out bacteria in culturing media/saline/drug solutions in labs and hospitals. On the other hand, mammalian cells are typically tens of micrometer in diameter. Red blood cells are smaller because they have to squeeze into small capillary blood vessels. Even then, the red blood cells are 7-8 micrometer in diameter. White blood cells are so much larger. So if you want to filter, you will filter out ALL the mammalian cells before stopping any bacteria / viruses...
Fighting infectious diseases is a monumental task! Even with hundreds of thousands of scientists working on it, we still cannot even cure a common flu. Viruses mutate like crazy. Before you can even figure out how to fight one kind of virus, it has mutated a thousand times and become something completely different from the one you have in mind... And the ability of a virus to incorporate into host cells is so effective that, to this date, we have not found anything that could even slow it down...
The best way to fight infectious diseases is still our own body. Our immune system is like a key maker while the infectious agents are like locks. The only way to open a lock is to make a key that matches the lock. So the key maker has to keep churning out new keys, hoping that one of them is a match. So when a lock keeps changing its key hole, the key maker has to play catch-up and chasing the lock and hope that he can figure out a key that would eventually fit the key hole before the lock changes again. This is exactly how our immune system functions. Upon infection, our immune system begins to manufacture T-cells, each of which is decorated with a different kind of antibody. So the idea is that one unique T-cell will eventually have the matching antibody that matches the antigen. Then this kind of T-cells will be mass produced, in an effort to mark as many antigen as possible. Other white blood cells then come in and attack those marked antigens, much like missiles attacking targets painted by lasers. that's why we get so exhausted when sick. Churning out all those T-cells is very energy costly.
So the best way is to figure out how to compliment this process, not to invent new ways. Getting flu shots is actually one way to do it. We carefully introduce remnant of viruses to our body and let our body churn out some T-cells with matching antibodies. then our body will keep some of these T-cells in stock as back-up. So next time, our body sees this kind of virus, it will mount attack much faster, thus preventing the virus from mutating again. And that's also why you want to get flu shots every year for at least 10 years. Every influenza virus is different and our immune system needs to be able to recognize all of it. They typically put 3 kinds of viruses in a flu shot every year. If you get flu shots for about 10 years, that would 30 different kinds of flu viruses. That should be enough to cover most kinds of flu viruses that you might find.