-  Mark the Record as Deceased (for Individuals or Faculty members, this is on the Bio1 tab; for Students or Applicants, this is on the Bio2 tab)
-  Create a new Relationship table entry called "Father - Deceased", "Mother - Deceased", etc and add this on the Relationship tab on the deceased Record's row
-  Create an Attribute called "Deceased" in Configuration, Attributes, (Record Type);  add this on the appropriate Record type so it can be used as a filter

As a general rule, the Deceased checkbox can be used as a filter frequently in Reports, Exports, etc.  It can always be selected as Criteria in a Query as well.