Antibody cells act just like a glue to grab antigens and transport them to somewhere isolated where they would be destroyed.
http://www.accessexcellence.org/RC/VL/GG/ecb/antibody_molecule.php
Virus are just genetic material inside a proteic shell. They're much small than average cells, and most of their proteins occur naturally in many cells, so injecting something to destroy these proteins can harm normal cells containing the same proteins. This is why is so hard to create antiviral drugs.
Bioinformatics/Pharmacology/Nanotechnology are trying to study a lot of things that could someday create effective solutions to these problems.