The Flory-Huggins interaction parameter (χ) measures the energetic interactions between polymer components, with high χ values driving the self-assembly of block copolymers (BCPs) into sub-10-nanometer microphases, a feature highly sought after in nanomanufacturing processes. Our study focuses on the area-selective directed self-assembly of well-defined lamella-forming BCPs on thin films. The process begins with coating a silicon oxide (SiO) wafer with a random copolymer layer, which is then crosslinked to create a neutral surface, ensuring an unbiased initial assembly environment. Next, a low χ BCP layer is applied. This low χ value is due to the initial protection of only one segment of the BCP. This allows for controlled deprotection later in the process, enabling precise localization of the lamella structures. The deprotection process removes the protecting groups from the protected segment, thereby increasing the χ parameter by enhancing the immiscibility between the blocks. To maintain the vertical orientation of the microdomains, a second random copolymer layer is applied on top of the BCP, forming a protective topcoat. This step is critical as it ensures the vertical alignment necessary for effective top-down observation and subsequent utilization of the layers. The low χ BCP is then converted to a high χ state through a deprotection process involving a photoacid generator. This conversion significantly increases the incompatibility between the blocks, driving the formation of a more well-defined lamella structure. A final annealing step perfects the lamella formation, ensuring the microdomains are correctly aligned and structured. This selective deprotection technique allows for precise control over the areas where the lamella structure is generated.