The objective of the present work is to describe a new mapping tool using anisotropic unstructured meshes to study mixing within a spatially periodic pipe flow. Instead of tracking the boundaries of elementary cell flow domains as it was done in the original mapping method established by Kruijt et al. (A.I.Ch.E. J. 47 (5) (2001a) 1005; Int. Polym. Process. 16 (2) (2001b) 151) and Galaktionov et al. (Comput. Fluids 30 (3) (2001) 271), the deformation of elementary triangles (only three nodal points) between the inlet and exit pipe cross-sections is followed. It is however necessary to adapt the initial mesh according to criteria which takes into account the spatial stretching and folding of fluid elements. The method developed is applied to the twisted curved pipes (TCP) three-dimensional (3D) flow. We show the evolution of concentration distributions along the TCP mixer for chaotic advection flow regimes. This method allows the emphasis of isolated unmixed regions (KAM islands). The flexibility of the method allows also the possibility of studying multiple stirring protocols, thus contributing to a better comprehension of the physical phenomena involved in chaotic mixing. The method developed is also applicable to 2D temporally periodic flows.