Methods and structures of a three-dimensional memory device are disclosed. In an example, the memory device includes a substrate having one or more first recesses in a first region and one or more second recesses in a second region. A liner layer is disposed over the sidewalls and bottom of the one or more first recesses in the first region and an epitaxially-grown material is formed in the one or more second recesses in the second region. One or more NAND strings are formed over the epitaxially-grown material disposed in the one or more second recesses, and one or more vertical structures are formed over the one or more first recesses in the first region.