Quantum-confined devices that manipulate single electrons in graphene are emerging as attractive candidates for nanoelectronics applications. Previous experiments have employed etched graphene nanostructures, but edge and substrate disorder severely limit device functionality. Here we present a technique that builds quantum-confined structures in suspended bilayer graphene with tunnel barriers defined by external electric fields that open a bandgap, thereby eliminating both edge and substrate disorder. We report clean quantum dot formation in two regimes: at zero magnetic field B using the energy gap induced by a perpendicular electric field and at B>0 using the quantum Hall ν = 0 gap for confinement. Coulomb blockade oscillations exhibit periodicity consistent with electrostatic simulations based on local top-gate geometry, a direct demonstration of local control over the band structure of graphene. This technology integrates single electron transport with high device quality and access to vibrational modes, enabling broad applications from electromechanical sensors to quantum bits.