Methods and apparatus for plugging cells of honeycomb structures are disclosed. A first method covers the honeycomb structure's end face with a mask having a body and plurality of sized openings positioned to oppose certain cell channels, wherein the outer edge of the body extends radially outwardly from the end face. A film also extends outwardly of the end face, and a plug of material is provided upon the film. The mask and film material are sealed to one another, and a force is applied to the film forcing the material through the mask and into the cells. Also disclosed is adhering a mask to a first end face of the honeycomb structure such that the mask has an outer portion that extends radially beyond an outer edge of the honeycomb; providing a volume of plugging material; clamping the outer portion between a first clamping portion and a second clamping portion; and transferring the plugging material into the honeycomb. Also disclosed are methods and apparatus for cutting the plugging material between the mask and a pre-plugging chamber to form a substantially planar surface thereon.