Structured illumination (SI) enhances image resolution and contrast by projecting patterned light onto a sample. In two-phase optical-sectioning SI (OS-SI), reduced acquisition time introduces residual artifacts that conventional denoising struggles to suppress. Deep learning offers an alternative to traditional methods; however, supervised training is limited by the lack of clean, optically sectioned ground-truth data. We investigate encoder-decoder networks for artifact reduction in two-phase OS-SI, using synthetic training pairs formed by applying real artifact fields to synthetic images. An asymmetrical denoising autoencoder (DAE) and a U-Net are trained on the synthetic data, then evaluated on real OS-SI images. Both networks improve image clarity, with each excelling against different artifact types. These results demonstrate that synthetic training enables supervised denoising of OS-SI images and highlight the potential of encoder-decoder networks to streamline reconstruction workflows.