This paper presents an improved methodology for the segmentation of the Air-Tissue boundaries (ATBs) in the upper airway of the human vocal tract using Real-Time Magnetic Resonance Imaging (rtMRI) videos. Semantic segmentation is deployed in the proposed approach using a Deep learning architecture called SegNet. The network processes an input image to produce a binary output image of the same dimensions having classified each pixel as air cavity or tissue, following which contours are predicted. A Multi-dimensional least square smoothing technique is applied to smoothen the contours. To quantify the precision of predicted contours, Dynamic Time Warping (DTW) distance is calculated between the predicted contours and the manually annotated ground truth contour. Four fold experiments are conducted with four subjects from the USC-TIMIT corpus, which demonstrates that the proposed approach achieves a lower DTW distance of 1.02 and 1.09 for the upper and lower ATB compared to the best baseline scheme. The proposed SegNet based approach has an average pixel classification accuracy of 99.3% across all the subjects with only 2 rtMRI videos (~180 frames) per subject for training.