Check the directory :
Generally em.ear is kept at this location if EM is added during server configuration.
If em.ear is not present at the above directory, then it means you have not added it during configuration. If you want to have it then you will have re-configure the server.
You will have to run config.sh from <MW_HOME>/oracle_common/common/bin/
1. Select the option Extend an existing Weblogic domain
2. Select the Weblogic Domain directory
3. Then select Oracle Enterprise Manager in the options.
If you select Oracle Enterprise Manager during configuration, the application em.ear gets created in applications directory. I am not sure why it is not there in your case. Did the first configuration end abruptly?
Instead of cleaning you can create a new domain afresh.