Topological Insulators (TIs) are a type of quantum material which have conducting surface states and insulating bulk states. Time-reversal symmetry (TRS) protects the gapless surface states from disorder and non-magnetic impurity backscattering. On the other hand, magnetic impurities like disorders such as anti-site and vacancy defects disrupt the TRS and result in intriguing phenomena like the quantum anomalous Hall effect, magnetoelectric effect, and magnetic monopole. The advantage of studying TIs in nanostructures is that their huge surface-to-volume ratio amplifies the features that are dominated by the surface. Bi2Se3, one of the most well-known TIs, has been the focus of a great deal of research due to its energy gap of 0.3 eV, which is greater than the room temperature energy scale. The main goal of this book chapter is to examine how strong disorder and magnetic doping affect the surface state of Bi2Se3 nanostructures. The exact magnetic and transport features in this system, which are backed by theoretical calculations, will be covered in depth.