creating complex structure
Is it possible in civicrm to create a structure where there is a main Branch this BRANCH has 4-5 sub branches BRANCH1, BRANCH2, BRANCH3, BRANCH4, BRANCH5 each of sub branches has 4-5 membership type.


Yes - just make a Membership Type and set each of the sub-Branches as the 'Organisation' for that Memb Type


  what type should i mention for custom fields like 'RESEARCHING SCHOLAR LINKS' where somebdy was member of Branch1 and new member is trying to be member of branch 2,.


Probably a Contact Reference field


  what should be the content type be given to custom fields so that relationships can be easily created/established.


Relationships do not have anything to do with Custom Fields. You can use Contact Reference custom fields to link one Contact to another, but it is more common to use Relationship Types