We report on the observation of self-organized stripe-like structures on the as-grown surface and in the bulk of (Nd,Eu,Gd)Ba$_2$Cu$_3$O$_y$ single crystals. The periodicity of the stripes on the surface lies between 500 and 800 nm. These are possibly the growth steps of the crystal. Transmission electron microscopy investigations revealed stripes of periodicity in the range of 20 to 40 nm in the bulk. From electron back scattered diffraction investigations, no crystallographic misorientation due to the nanostripes has been found. Scanning tunneling spectroscopic experiments revealed nonsuperconducting regions, running along twin directions, which presumably constitute strong pinning sites.