A method of processing a semiconductor structure may include preparing a vertical channel memory structure for filling of a physical isolation trench formed therein. The physical isolation trench may be formed between active structures adjacent to each other and extending in a first direction. The active structures may have channels adjacent to sides of the active structures that are opposite to sides of the active structures that are adjacent to the physical isolation trench. The method may further include filling the physical isolation trench in connection with application of a multi-dielectric layer (ex. an oxide-nitride-oxide (ONO) layer), a polysilicon liner and/or an oxide film. A corresponding apparatus and method for integrating such a structure with a planar periphery are also provided.