I think what you mean by “base paths” is the path that Apigee implicitly appends to the target URL. In Apigee-speak this is the “path suffix”. To prevent Apigee’s default behavior, attach a policy in the Target request flow (can be PreFlow , or PostFlow) that sets the context variable target.copy.pathsuffix, to false.
Example policy
<AssignMessage name='AM-NoCopyPath'>
<AssignVariable>
<Name>target.copy.pathsuffix</Name>
<Value>false</Value>
</AssignVariable>
</AssignMessage>
If you mean something other than this, please elaborate.