How to remove alpha from textures

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Import the image to Krita and right click -> Alpha into Mask.

Then delete the “Transparency” mask.

Export PMX as FBX for Clip Studio Modeler

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Convert the material to Blender, and export FBX with these options:

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You should setup physics in PmxEditor, because changing values is easier.

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If your material is using BSDF nodes or Emission, you can convert them into MMD shader (MMDShaderDev).

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Adjust MMD Material > Alpha to add transparency.