In the southern section Northampton beat Peterborough thanks to a Silver goal from Lawrie Dudfield, while Colchester scored a winner against Wycombe with a goal in the last minute of extra time.
Southend strolled to a 3-0 win over Luton.
The draw for the regional finals will take place on Sky Sports' Soccer AM programme on Saturday morning.
Northern Quarter finals:
Bury 0 Scunthorpe 1 (Silver goal)
Carlisle 0 Sheffield Wednesday 3
Halifax P Lincoln P (postponed due to fog)
Stockport 0 Blackpool 1 (AET)
Southern Quarter finals:
Northampton 2 Peterborough 1 (Silver goal)
Southend 3 Luton 0
Wycome 2 Colchester 3 (AET)