In general you have to create a plug point for custom password encryption in order to encrypt and decrypt all passwords in WebSphere® Application Server that are currently encoded or decoded using Base64-encoding
For more information, you can check the following topic:
http://www.ibm.com/support/knowledgecenter/SSAW57_8.5.5/com.ibm.websphere.nd.doc/ae/csec_plugpoint_custpass_encrypt.html