If they're just certificate authorities you're looking to import into a Trusted Roots or Intermediate Roots container, just change the extension to
.crt and Windows should be able to handle it with little issues.
If the .pem files are part of .pem/.key file pairs, then you'll have to convert them into a
.pfx file before Windows can touch them. OpenSSL can be used to create such an archive.
openssl pkcs12 -export -out newfile.pfx -inkey privcert.key -in pubcert.pem -certfile CARoots.pem
It will prompt you for a password to protect the file with. Use that password when importing into IIS.