Mutagen Man: Simple, direct, and highlights the core power.
The Alchemist: Evokes a sense of transformation and mastery over matter.
Form Shifter: Focuses on the ability to change shape and form.
Matter Weaver: Suggests a skillful manipulation of matter, almost artistic in nature.
The Transmuter: A straightforward and powerful-sounding name.
Elementalist: Broader than just matter manipulation, but still relevant if the powers include elemental transmutation.
Molecular Maestro: Sophisticated and implies precise control over matter at a microscopic level.
The Metamorph: Classic and evocative of shape-shifting and transformation.
Atomic Architect: Suggests the ability to build and reshape matter at the atomic level.
The Flux: A more abstract name, suggesting constant change and instability.
Chronosmith: If the matter manipulation includes time-based effects, this name would be fitting.
Reality Bender: A more powerful-sounding name, implying a wider range of abilities.
The Sculptor of Worlds: A grandiose name, suitable for a hero with immense power.
Terraformer: If the matter manipulation is used to reshape landscapes.
The Quantum Weaver: Suggests manipulation at a subatomic level.
Names incorporating specific elements: If the matter manipulation involves specific elements, consider names like "Pyromancer" (fire), "Cryomancer" (ice), "Geomancer" (earth), etc., but combine them with a descriptor like "Master" or "Lord" to indicate their control over matter. For example, "Pyromancer Master" or "Lord of the Cryo-Form."
These names offer a variety of styles and tones, from straightforward to more evocative and dramatic. The best choice will depend on the specific tone and style of your project.