Cosmic Ray (CR) interactions with the dense gas inside Giant Molecular Clouds (GMCs) produce neutral pions, which in turn decay into gamma rays. Thus, the gamma ray emission from GMCs is a direct tracer of the cosmic ray density and the matter density inside the clouds. Detection of enhanced TeV emission from GMCs, i.e., an emission significantly larger than what is expected from the average Galactic cosmic rays illuminating the cloud, can imply a variation in the local cosmic ray density, due to, for example, the presence of a recent accelerator in proximity to the cloud. Such gamma-ray observations can be crucial in probing the cosmic ray distribution across our Galaxy, but are complicated to perform with present generation Imaging Atmospheric Cherenkov Telescopes (IACTs). These studies require differentiating between the strong cosmic-ray induced background, the large scale diffuse emission, and the emission from the clouds, which is difficult to the small field of view of present generation IACTs. In this contribution, we use H.E.S.S. data collected over 16 years to search for TeV emission from GMCs in the inner molecular galacto-centric ring of our Galaxy. We implement a 3D FoV likelihood technique, and simultaneously model the hadronic background, the galactic diffuse emission and the emission expected from known VHE sources to probe for excess TeV gamma ray emission from GMCs.