  Topological insulators are distinguished from normal insulators by their bulk
insulating gap and odd number of surface states connecting the inverted
conduction and valence bands and showing Dirac cones at the time-reversal
invariant points in the Brillouin zone. Bi-based three-dimensional strong
topological insulator materials, Bi$_2$Se$_3$ and Bi$_2$Te$_2$, are known as
high temperature topological insulators for their relatively large bulk gap and
have one simple Dirac cone at the $\Gamma$ point. In spite of their clear
surface state Dirac cone features, the Dirac point known as a Kramers point and
the topological transport regime is located below the bulk valence band
maximum. As a result of a non-isolated Dirac point, the topological transport
regime can not be acquired and there possibly exist scattering channels between
surface and bulk states as well. In this article we show that an ideal and
isolated Dirac cone is realized in a slab geometry made of Bi$_2$Se$_3$ with
appropriate substitutions of surface Se atoms. In addition to Dirac cone
engineering by surface atom substitutions, we also investigate Bi$_2$Se$_3$
thin films in terms of thickness and magnetic substitutions, which can be
linked to applications of spintronics devices.
