First, nothing will totally make the holes invisible. You can take a number of steps to make them less obvious. I have a different brand boot but the issues were the same. Embossed, instead of glued and stitched logos made removal of mine impossible. I settled for covering mine with thin pieces of gray suede leather patches since there are similar textures on the actual boots. The holes from stitching are harder. There are several options to reduce the look. First remove as much thread as possible. Some stitches can be tenacious and I melted remnants away with a small butane torch. You can use a cigarette lighter instead. To fill holes use one of the following. Black acrylic artist tube paint,(its thicker). Buy a leather repair kit which has a similar material in small pots. Some use heat from a small iron to set the material. Or,as with the suede remedy, cover the holes with thin smooth garment leather cut to a logical looking shape to mask the area. You can also use quick setting epoxy applied with a toothpick to each hole. If any mounds above the surface,use a single edge razor blade or scalpel to shave it flush. If any of your repairs don't match,paint the boot. Don't use regular paint. Many auto parts stores like Auto Zone stock vinyl/leather paint in black.The spray paint comes in flat or gloss versions. If your raised logo is glued on,you may choose to shave it flat with a blade and cover with leather. If it is glued there may be residue you can't get off if you remove it. If you want less expensive options than new leather you can cheat with fake stuff from the fabric store or try some thrift shops for leather pants (even ladies) or coats. Hope this helps.