Not sure if I'm following you; did you deleted datafiles at O/S level without telling Oracle about your intentions?

If the answer is yes...

1- Connect as follows...

sqlplus /nolog
conn sys as sysdba
--hit enter
shutdown abort;
startup nomount;

2- Put offending datafiles offline.

3- Set offending tablespace offline -use immediate option

4- Drop offending tablespace

5- Shutdown then startup

Depending on your particular setup and content of your affected tablespace/s you may bump into different issues but that's what you have to do... in a nut shell.