A systematic estimation of the line of sight depth in the disk and bar regions of the Large and Small Magellanic Clouds (LMC and SMC) using red clump stars is presented. We used the red clump stars from the photometric data of the Optical Gravitational Lensing Experiment (OGLE II) survey and the Magellanic Cloud Photometric Survey (MCPS) for both the Clouds to estimate the depth. The observed dispersion in the magnitude and colour distribution of red clump stars is used to estimate the depth, after correcting for population effects, internal reddening within the Clouds and photometric errors.The observed dispersion due to the line of sight depth ranges from 0.023mag, to 0.45mag (a depth of 500pc to 10.4kpc) for the LMC and, from 0.025 to 0.34mag (a depth of 670 pc to 9.53kpc) for the SMC. The minimum value corresponds to the dispersion that can be estimated due to errors. The depth profile of the LMC bar indicates that it is flared. The average depth in the bar region is 4.0±1.4kpc. The northern disk is found to have depth (4.17±0.97kpc) larger than the southern part of the disk (2.63±0.8kpc). There is no indication of depth variation between the eastern (2.8±0.92kpc) and the western (3.09±0.99kpc) disk. The average depth for the disk is 3.44±1.16kpc. The SMC is found to have larger depth than the LMC. In the case of the SMC, the bar depth (4.90±1.23kpc) and the disk depth (4.23 ±1.48kpc) are found to be within the standard deviations. A prominent feature in the SMC is the increase in depth near the optical center. The averaged depth profile near the center resembles a structure like a bulge. The large dispersions estimated in the LMC bar and the northern disk suggest that the LMC either has large depth and/or different stellar population in these regions. The halo of the LMC (using RR Lyrae stars) is found to have larger depth compared to the disk/bar, which supports the existence of an inner halo for the LMC. On the other hand, the estimated depths for the halo (RR Lyrae stars) and disk are found to be similar, for the SMC bar region. Thus, increased depth and enhanced stellar as well as HI density near the optical center suggests that the SMC may have a bulge.