The intelligent handling of deformable objects by robotic manipulators has enabled the automation of various delicate or labour-intensive tasks, but still faces many challenges when it comes to more complex situations. In particular, the lack of a general framework to manage deformation makes it difficult to manipulate unknown objects, especially in the 3D case. This work aims to provide a path forward to solve some of the challenges pertaining to the robotic manipulation of deformable objects and integrate these solutions in a flexible system able to manipulate various deformable objects in a taskindependent way.