Wavefront shaping enables control over optical fields for applications ranging from imaging to photonic information processing. While conventional wavefront shaping relies on free-space systems comprising bulk optical components, compact and fully integrated approaches are comparatively unexplored. Here, we introduce a concept based on a single multimode waveguide with distributed thermo-optic perturbations for controlling multimode propagation. We develop a differentiable physical model and numerically demonstrate shaping the outgoing wavefront and programmable linear optical transformations, using gradient-based optimization. We achieve diffraction-limited focusing with 20 spatial modes and show that the theoretical focusing limit can be retained while maintaining more than 99% of the input optical power. We extend this approach to complete input–output transformations and implement Sylvester–Hadamard matrix operations with dimensions up to 32×32 with correlations exceeding 99%. Reducing the number of tunable elements requires stronger individual perturbations, resulting in stronger and broader mode coupling that extends beyond the target modes. To mitigate this effect, we consider ancillary modes and realize a 4×4 transformation that reaches 93.8%±4.8% correlation with only 5N² tunable elements, where N=4 denotes the number of spatial modes. The best-performing realization reaches 98.3% correlation with the target. Our results demonstrate that thermo-optic control of multimode waveguides offers an approach to fully-integrated wavefront shaping and programmable linear optical transformations, with potential applications in classical and quantum photonic processing