Q: What does MODIS data reflectance values (MOD13Q1) mean? Several publications suggest filtering MODIS data (in my case MOD13Q1) prior to use. They recommended to filter out pixels having blue reflectance more than 10%, but what 10% here means? is it 10% of the total possible value for blue reflectance or 10% or the total reflected over the whole spectrum?
Any advices?

A: you don't need to make an atmospheric correction for the MOD13Q1 product because it was generated by the Maximum Value Composite method,this means that among 16 rasters (16 days) the reflectance value for a pixel is the least contaminated by clouds, but also the one with the maximum value.
They provide information on the quality of data VI (vegetations index):
the MOD13Q1 Pixel Reliability, and MOD13Q1 VI Quality rasters provide informations about the quality of data VI (vegetations index):
Refer to TABLE 1: MOD13Q1 Pixel Reliability and TABLE 2: MOD13Q1 VI Quality in the https://lpdaac.usgs.gov/products/modis_products_table/mod13q1
If you use Daily products like MOD09GQ (MODIS Terra Surface Reflectance Bands 1–2 /250m), the atmospheric correction can be logical.

A: I got the answer! The reflectance values are already in percentage. In MODIS evi they are fractions of 1 multiplied by  10000, i.e. 0-10000. The 10% blue reflectance values are equal to 1000 in the MODIS raster image.
