The paper presents a novel method called Overlap-Controlled Multi-Scan (OCMS) for precise control of the refractive index (RI) profile and cross-sectional shape of 3D waveguides in glass using laser-direct lithography. This method allows for high spatial resolution and precise control of the RI distribution, enabling variable mode-field distribution, robust and broadband coupling, and dispersionless LP1-mode conversion of supercontinuum pulses with minimal deviation. The OCMS technique overcomes the limitations of traditional planar lithography and femtosecond laser direct writing (FLDW) by accurately managing thermal accumulation effects within the laser irradiation region. The method is versatile and applicable to various glasses, including commercial screen glasses and fused silica. The authors demonstrate the effectiveness of the OCMS method by fabricating waveguides with step, GRIN, "W"-like, and "U"-like profiles, achieving submicron spatial resolution and RI resolution. They also show that the OCMS waveguides can be used to realize arbitrary spatial mode manipulation of ultra-short laser pulses and ultra-broadband supercontinuum, with excellent mode circularity and low coupling losses. The OCMS-based 3D waveguide coupler exhibits high mode coupling ratios and mode purity over a broadband range, making it suitable for mode-selective 3D waveguide circuits. Additionally, the OCMS waveguides can be used to route ultrashort pulses and broadband supercontinuum in the time domain, transforming them into higher-order modes with negligible spatiotemporal distortion. The paper highlights the advantages of 3D glass chips in delivering and manipulating linear and nonlinear laser light with ultra-broadband capabilities, representing a significant advancement in the miniaturization of benchtop optical systems into chip-scale devices.The paper presents a novel method called Overlap-Controlled Multi-Scan (OCMS) for precise control of the refractive index (RI) profile and cross-sectional shape of 3D waveguides in glass using laser-direct lithography. This method allows for high spatial resolution and precise control of the RI distribution, enabling variable mode-field distribution, robust and broadband coupling, and dispersionless LP1-mode conversion of supercontinuum pulses with minimal deviation. The OCMS technique overcomes the limitations of traditional planar lithography and femtosecond laser direct writing (FLDW) by accurately managing thermal accumulation effects within the laser irradiation region. The method is versatile and applicable to various glasses, including commercial screen glasses and fused silica. The authors demonstrate the effectiveness of the OCMS method by fabricating waveguides with step, GRIN, "W"-like, and "U"-like profiles, achieving submicron spatial resolution and RI resolution. They also show that the OCMS waveguides can be used to realize arbitrary spatial mode manipulation of ultra-short laser pulses and ultra-broadband supercontinuum, with excellent mode circularity and low coupling losses. The OCMS-based 3D waveguide coupler exhibits high mode coupling ratios and mode purity over a broadband range, making it suitable for mode-selective 3D waveguide circuits. Additionally, the OCMS waveguides can be used to route ultrashort pulses and broadband supercontinuum in the time domain, transforming them into higher-order modes with negligible spatiotemporal distortion. The paper highlights the advantages of 3D glass chips in delivering and manipulating linear and nonlinear laser light with ultra-broadband capabilities, representing a significant advancement in the miniaturization of benchtop optical systems into chip-scale devices.