Trying to turn a sprite into a 3d printable pin. Imported with ImportPixelArt Extension, manifolding /w print toolbox doesn't work - parts disappear!

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First post, still a blender noob. apologies. I don't have a multicolor 3d printer, so I am making seperate blender files for different pieces. The file in pic is the pin's base, which is why it has parts jutting up. I intend to glue the other pieces into those holes. Just one problem. The moment I try to manifold the base, a bunch of random parts disappear. See upper pic. How do I fix this? I also use mesh repair & made sure to ctrl+j the whole thing if that narrows things down. Any help is greatly appreciated. https://preview.redd.it/xtp7cv4a24uh1.png?width=790&format=png&auto=webp&s=a113d19d419d9baf0e00491ce291fa2603850df1 https://preview.redd.it/d0ov6sbzy3uh1.png?width=872&format=png&auto=webp&s=3cdaf3f99a678c7b3e50a76428c32abc80219946   submitted by   /u/Ok-Pay-9107   to   r/blender [link]   [comments]