Extracting 3D shape of deforming objects in monocular videos, a task known as non-rigid structure-from-motion (NRSfM), has so far been studied only on synthetic datasets and controlled environments. Typically, the objects to reconstruct are pre-segmented, they exhibit limited rotations and occlusions, or full-length trajectories are assumed. In order to integrate NRSfM into current video analysis pipelines, one needs to consider as input realistic -thus incomplete- tracking, and perform spatio-temporal grouping to segment the objects from their surroundings. Furthermore, NRSfM needs to be robust to noise in both segmentation and tracking, e.g., drifting, segmentation leaking'', optical flowbleeding'' etc. In this paper, we make a first attempt towards this goal, and propose a method that combines dense optical flow tracking, motion trajectory clustering and NRSfM for 3D reconstruction of objects in videos. For each trajectory cluster, we compute multiple reconstructions by minimizing the reprojection error and the rank of the 3D shape under different rank bounds of the trajectory matrix. We show that dense 3D shape is extracted and trajectories are completed across occlusions and low textured regions, even under mild relative motion between the object and the camera. We achieve competitive results on a public NRSfM benchmark while using fixed parameters across all sequences and handling incomplete trajectories, in contrast to existing approaches. We further test our approach on popular video segmentation datasets. To the best of our knowledge, our method is the first to extract dense object models from realistic videos, such as those found in Youtube or Hollywood movies, without object-specific priors.