Measuring and monitoring the height of vegetation provides important insights into forest age and habitat quality. These are essential for the accuracy of applications that are highly reliant on up-to-date and accurate vegetation data. Current vegetation sensing practices involve ground survey, photogrammetry, synthetic aperture radar (SAR), and airborne light detection and ranging sensors (LiDAR). While these methods provide high resolution and accuracy, their hardware and collection effort prohibits highly recurrent and widespread collection. In response to the limitations of current methods, we designed Y-NET, a novel deep learning model to generate high resolution models of vegetation from highly recurrent multispectral aerial imagery and elevation data. Y-NET’s architecture uses convolutional layers to learn correlations between different input features and vegetation height, generating an accurate vegetation surface model (VSM) at $1\times 1$ m resolution. We evaluated Y-NET on 235 km${}^2$ of the East San Francisco Bay Area and find that Y-NET achieves low error from LiDAR when tested on new locations. Y-NET also achieves an $R^2$ of 0.83 and can effectively model complex vegetation through side-by-side visual comparisons. Furthermore, we show that Y-NET is able to identify instances of vegetation growth and mitigation by comparing aerial imagery and LiDAR collected at different times.