The evaluation of scatterometry for monitoring intended variations in innovative scatterometry targets that mimic nonuniformities potentially caused by multibeam Maskless Lithography (MEB-ML2) is presented. Specialized scatterometry targets consisting of lines and spaces were produced that have portions exposed using the nominal, or POR (Process of Record), dose, and portions exposed with a slightly different dose. These exposure plans created targets with different line CDs (critical dimensions). Multiple target designs were implement, each with a different combination of magnitude of CD shift and size of the region containing lines with a shifted CD. The scatterometry, or OCD (Optical Critical Dimension), spectra show clear shifts caused by the regions with shifted CD, and trends of the scatterometry results match well with trends of the estimated CD as well as the trends produced by measurements using a critical dimension scanning electron microscope (CD-SEM) system. Finally, the OCD results are correlated to the CD-SEM measurements. Taking into account resist morphology variations across the wafer, correlations between OCD and CD-SEM of the weighted average CD across the various targets are shown to be very good. Correlations are done using the rigorous TMU analysis methodology. Due to the different targeted CD values within each scatterometry structure, a new methodology for estimating the error of the CD-SEM measurements for nominally non-uniform targets is presented. © 2017 SPIE.