Self-aligned trench filling is used to isolate devices in high-density integrated circuits. A deep, narrow trench isolation region is formed in a substrate between devices. The trench region includes two trench portions. A first trench portion, located above a second trench portion, is filled with a deposited dielectric. The second trench portion is filled with a grown dielectric. Filling the lower trench portion by growing a dielectric material provides for an even distribution of dielectric material within the lower portion. Filling the upper trench portion by depositing a dielectric material provides for an even distribution of material in the upper portion while also protecting against encroachment of the dielectric into device channel regions, for example. Devices can be fabricated by etching the substrate to form the trench region after or as part of etching one or more layers formed above the substrate for the device. This can ensure alignment of the gate and channel regions of a device between trench isolation regions.