The research project “Mouseion Topos” (in English: “Museums Place”), focusing on traditional local settlements situated at three Aegean islands, aims to contribute to the promotion of their physiognomy and intangible cultural heritage by connecting regional museums with each settlement. The present article, part of the project’s initial phase, via the application of the HERMeS methodology (version 1 and 2) and the development of the associate digital documentation tools, identifies and records the architectural and urban elements influenced by each settlement’s intangible cultural heritage as listed by UNESCO and presented by their corresponding museums. The research findings revealed connections between the museums’ content and the documented tangible heritage based on the formulated conceptual and heatmaps, which can be used at the early design stages of the current project’s interactive applications, especially in mobile tours. Finally, the research findings verify that despite the limitations and issues for further research, the introduced HERMeS methodology and digital tools are reliable and contribute to the respective field’s theory. The paper also provides beneficial deliberation on digital architectural heritage documentation methods and interactive technologies, highlighting points and areas of interest that the tourist industry, technology designers, museum curators, and architects can employ.