ZnO nanorods (NRs) arrays doped with a large concentration of Mn synthesized by aqueous chemical growth and were characterized by SEM, photoluminescence, Raman scattering, magnetic force microscopy (MFM). By comparison of spectra taken on pure and Mn-doped ZnO NRs, a few new Raman impurity-related phonon modes, resulting from the presence of Mn in the investigated samples. We also present a vibrational and magnetic characterization of individual lying nanorods using Raman and MFM imaging. Confocal scanning micro-Raman mapping of the spatial distribution of intensity and frequency of phonon modes in single Mn-doped ZnO NRs nanorods is presented and analyzed for the first time. Mn-related local vibrational modes are also registered in Raman spectra of the single nanorod, confirming the incorporation of Mn into the ZnO host matrix. At higher Mn concentration the structural transformation toward the spinel phase ZnMn2O4 and Mn3O4 is observed mainly in 2D bottom layers. MFM images of Mn-doped ZnO NR arrays and single nanorod were studied in nanoscale at room temperature and demonstrate magnetic behavior. The circular domain magnetic pattern on top of single nanorod originated to superposition of some separate domains inside rod. This demonstrates that long-range ferromagnetic order is present at room temperature. Aligned Mn-doped ZnO NRs demonstrates that long-range ferromagnetic order and may be applied to future spintronic applications.Electronic supplementary materialThe online version of this article (doi:10.1186/s11671-017-2127-4) contains supplementary material, which is available to authorized users.