The subject disclosure is directed towards layered substrate structures with aligned optical access to electrical devices formed thereon for laser processing and electrical device tuning. According to an embodiment, a layered substrate structure is provided that comprises an optical substrate having a first surface and a second surface and a patterned bonding layer formed on the second surface that comprises a bonding region and an open region, wherein the open region exposes a portion of the second surface. The layered substrate structure further comprises a device chip bonded to the patterned bonding layer via the bonding region and comprising at least one electrical component aligned with the optical substrate and the open region. The at least one electrical component can include for example, a thin film wire, an air bridge, a qubit, an electrode, a capacitor or a resonator.