Disclosed herein are methods for manufacturing devices by combining mask-based and maskless lithography. For example, in some embodiments, a method of forming a semiconductor device may include performing a mask-based lithographic process on a substrate having one or more layers disposed thereon to form a set of mask-based features in a first layer of the one or more layers and performing a maskless lithographic process on the substrate to form a set of maskless features. Such a method allows to benefit from the advantages of both mask-based and maskless lithographic techniques. For example, mask-based lithography may be used to form most of the features while maskless lithography may be used to modify, delete, or add a relatively small number of features. In this manner, high throughput may be achieved by employing mask-based lithography while providing the flexibility in the features allowed by the use of maskless lithography.