A custom profile defines an empty node on a system. The purpose of this profile is to define a node on a system to be federated to a cell for central management. As you create the profile, you will have the option to federate the node to a cell during the wizard, or to simply create the profile for later federation. Before you can federate the custom profile to a cell, you will need to have a running deployment manager.
You might want to create a custom profile when your end goal is create cluster, Lets say if you want to create a horizontal cluster on 3 machines then you might want to create Application Server profile on Machine 1 and custom profile on Machine 2 and 3. Then you can configure application server on Machine 1 and use it as a template for creating cluster and add Machine 2 and Machine 3 nodes in the cluster. The WAS process will take care of creating application servers based on your machine 1 configuration on other 2 machines.
Follow the Profile Management wizard to create custom profile like this
If you dont want to federate the node at the time of profile creation Check the "Federate this node later" checkbox