Monte Carlo (MC) dose calculation has appeared in primary commercial treatment planning systems (TPS) as well as various secondary (in-house) platforms. MC promises smaller dose uncertainties, particularly in patients with low density and bony heterogeneities and metal implants. Newly developed dual energy computed tomography (DECT) and metal artifact reduction (MAR) methods compliment MC capabilities. However, there are no publications to date reporting how proton therapy centers implement these new technologies, and a consensus is required for their inclusion in clinical trials. A survey was designed to query key clinical parameters: scope of MC utilization, validation methods in homogeneous and heterogeneous phantoms, clinical site-specific imaging guidance, proton range uncertainties, and how metal implants are handled. A national survey was distributed to 29 operational US proton therapy centers on 5/13/19 and updated on 10/18/19. We received responses from 25 centers (86% participation). Commercial MC is most often used for primary plan optimization or primary dose evaluation, while in-house MC is used more frequently as secondary dose evaluation. This suggests that if an institution has a commercial MC system, they are using it as their primary dose calculation and optimization engine. Based on the survey, MC is used infrequently for GU and GYN, compared to other disease sites (P<0.0016). Other than IROC and electronic density phantoms, there is no consensus over the use of heterogeneous phantoms or QA measurement methods, although 3 mm/3% is typically used in patient QA using homogeneous phantoms. MC is used (80%) for plans with apertures or range shifters. Although most centers use 3-3.5% for range uncertainties, a few centers use 5% range uncertainty for lung treatment to account for uncertainty caused by low-density heterogeneity. Although many centers have published DECT research, only 3/25 centers have implemented DECT clinically, either in the TPS or to override implant materials. Most centers (64%) treat patients with metal implants case-by-case, with a variety of methods reported. 24 centers (96%) override the surrounding tissue artifacts; however, there is no consensus on using MAR images, determining metal dimension, or assigning materials density and stopping powers among proton centers. The use of MC for primary dose calculation and optimization is positive for clinical trials, where MC is required or encouraged for several disease sites. MC may be unnecessary for homogeneous anatomy, such as GU and GYN. While variable methods exist to determine metal implant material density and dimensions, most centers override surrounding tissues. DECT has rarely been implemented clinically for patient modeling in MC, and there is no consensus over the use of heterogeneous phantoms, nor the use of metal artifact reduction images for metal implants. Standardization for the use of these advanced technologies is encouraged.