Answer:
After the microorganisms are killed the tools are kept in sterile plastic bags which is sealed so that it cannot come in contact with the environment further. If the tools treated for killing microorganism will expose to environment it can allow microorganism to spread and infect others.
Plastic bags also protects tools from humidity and moisture and protect the tool from contamination. It may be possible that some of the traces of microorganism are left on the tool which can be recover later for future research purposes.
Hence, tools are required to kept in plastic bags after all the microorganisms are killed.