No, you won't be safe saving infected files into a external hdd and then reinfecting your self. Format your who computer and let got the files too.
How do I do to recover my wallet.dat in this case
?first export private keys. Print on paper or make foto with (non-internet) camera. clean all USB memories, external HDDs and all other flash memory or memory you used on this computer. Remember: If you burned CDs/DVDs in recent times: DONT USE ANYMORE!
then totally clean the computer -> format HDD SECURE! (= more than 5 time with rewrite on HD) & install SECURE OS (NO windows). If you use again windows because you have to, make sure its first secured before you install anything. DO NOT USE PRECOMPILED wallets of other coins, etc. Always try compile your things alone (from REVIEWED sourcecodes only) if its from not trusted developer. Most keylogger, wallet-stealer, etc. ARE NOT IN virus-database. In many cases its only small backdoor added to sourcecode of cryptocoins-apps, wallets & Co. TRUST NOBODY!
when the secure & clean computer is ready you simple install BTC wallet (ONLY from TRUSTED source) and import the keys.
sorry for your loss!