Recently, Topological Hall Effect (THE) has been unravelled in various perovskite iridate, ruthenate and manganite interfaces, suggesting the presence of magnetic Skyrmion-like bubbles. Among the materials and sample structures investigated so far, the physical properties were not free from influences of substrates, which are templates for crystalline epitaxial growth. Additional contributions of Dzyaloshinskii-Moriya Interaction or Berry curvatures by the substrates may originate from several structural factors such as in-plane strain, octahedral rotation or terminations. In this report, we employ the water-soluble Sr3Al2O6 sacrificial buffer layer to prepare freestanding SrRuO3/SrIrO3 heterostructures with high-quality interfaces, and THE-like humps are observed up to 90 K. Analysing the Hall signal with the rotation of magnetic field direction suggests there are magnetically decoupled regions. This scheme also paves the way for several magnetic texture imaging techniques in transmission mode for future studies.