Ambiguities are common in human-robot interaction, especially when a robot follows user instructions in a large collocated space. For instance, when the user asks the robot to find an object in a home environment, the object might be in several places depending on its varying semantic properties (e.g., a bowl can be in the kitchen cabinet or on the dining room table, depending on whether it is clean/dirty, full/empty and the other objects around it). Previous works on object semantics have predicted such relationships using one shot-inferences which are likely to fail for ambiguous or partially understood instructions. This paper focuses on this gap and suggests a semantically-driven disambiguation approach by utilizing follow-up clarifications to handle such uncertainties. To achieve this, we first obtain semantic knowledge embeddings, and then these embeddings are used to generate clarifying questions by following an iterative process. The evaluation of our method shows that our approach is model agnostic, i.e., applicable to different semantic embedding models, and follow-up clarifications improve the performance regardless of the embedding model. Additionally, our ablation studies show the significance of informative clarifications and iterative predictions to enhance system accuracies.