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The surface of quasi-hexagonal reconstructed Au(100) is used as the template for monolayer pentacene (PEN) self-assembly. The system is characterized by means of scanning tunneling microscopy at room temperature and under an ultra-high vacuum. A new modulated pattern of molecules with long molecular axes (MA) arranged along hex stripes is found. The characteristic features of the hex reconstruction are preserved herein. The assembly with MA across the hex rows leads to an unmodulated structure, where the molecular layer does not recreate the buckled hex phase. The presence of the molecules partly lifts the reconstruction—i.e., the gold hex phase is transformed into a <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>(</mo><mn>1</mn><mo>×</mo><mn>1</mn><mo>)</mo></mrow></semantics></math></inline-formula> phase. The arrangement of PEN on the gold <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>(</mo><mn>1</mn><mo>×</mo><mn>1</mn><mo>)</mo></mrow></semantics></math></inline-formula> structure is the same as that of the surrounding molecular domain on the reconstructed surface. The apparent height difference between phases allows for the distinction of the state of the underlying gold surface.