You can try the following:
cd NMSROOT/objects/data/cmf/cmic/mst-templates
NMSROOT/lib/jre/bin/java -cp NMSROOT/MDC/tomcat/shared/lib/xerces.jar:NMSROOT/objects/log4j/1.1.3/log4j.jar:NMSROOT/MDC/tomcat/shared/lib/MICE.jar:NMSROOT/MDC/tomcat/shared/lib/NATIVE.jar:NMSROOT/lib/classpath/cmic.jar:NMSROOT/lib/classpath:NMSROOT/MDC/tomcat/webapps/cwhp/WEB-INF/classes com.cisco.nm.cmf.cmic.registry.CMICApplicationRegistry administration.1.0 0 register
NMSROOT is the path into which you installed CiscoWorks.