Enterprise Manager deleting a target manually

First stop the agent.

./emctl stop agent
Oracle Enterprise Manager Cloud Control 13c Release 1  
Copyright (c) 1996, 2015 Oracle Corporation.  All rights reserved.
Stopping agent ... stopped.

emcli login -username=sysman
emcli sync
emcli delete_target -name="em-host.domain.com:3872" -type="oracle_emd" -delete_monitored_targets

Now Uninstall the agent

export ORACLE_HOME=export ORACLE_HOME=/u01/app/agent/core/12.1.0.2.0
$ORACLE_HOME/oui/bin/runInstaller -deinstall -removeallfiles

# OR remove manually 
rm -r /opt/agent13_1
rm /etc/init.d/gcstartup /etc/rc3.d/*gcstartup