See this code in Google Earth Engine: https://code.earthengine.google.com/50699c2eaa1a873ccd28f26c583c5a45

Fmask on Google Earth Engine

var polygon = ee.Geometry.Polygon([[
  [-119.33364769821117, 46.05123532178373],
  [-119.3233620672313, 45.869732769408905],
  [-119.04111088542663, 45.873079023065166],
  [-119.0396574679861, 46.045448840018565]
]]);
var landsat8 = ee.ImageCollection("LANDSAT/LC8_L1T_TOA_FMASK");

//
// Masking Clouds with Fmask
//

var PIXEL_SCALE = 30; // Meters. Resolution of most Landsat 8 bands
var PIXEL_AREA = PIXEL_SCALE * PIXEL_SCALE; // Square meters.

// Fmask classification values
var FMASK_CLEAR_GROUND = 0;
var FMASK_WATER = 1;
var FMASK_CLOUD_SHADOW = 2;
var FMASK_SNOW = 3;
var FMASK_CLOUD = 4;

var mosaic = landsat8
  .filterBounds(polygon)
  .filterDate('2016-08-01', '2016-08-30')
  .mosaic();

// Update the mask on our mosaic to mask cloud and cloud shadow pixels
var fmask = mosaic.select('fmask');
var cloudMask = fmask.neq(FMASK_CLOUD).and(fmask.neq(FMASK_CLOUD_SHADOW));
var maskedMosaic = mosaic.updateMask(cloudMask);


Map.addLayer(fmask, {min:0, max:4, palette:'green, blue, black, cyan, white'}, 'Fmask');
Map.addLayer(maskedMosaic.select('B4'), {min:0, max:0.5, palette:'yellow, green'}, 'Masked NIR');
Map.setCenter(-119.34, 45.97, 8);

//
// Calculating Region Cover Statistics
//

// Calculate the number of pixels of each classification in our polygon
var regionCoverHistogram = mosaic.select('fmask')
  .reduceRegion(ee.Reducer.frequencyHistogram(), polygon, PIXEL_SCALE);
print('Fmask class pixel count within region', regionCoverHistogram);


var waterPixelCount = ee.Dictionary(regionCoverHistogram.get('fmask'))
  .get(FMASK_WATER.toString());
  
var waterArea = ee.Number(waterPixelCount).multiply(PIXEL_AREA);
print('Water Area (sq meters) in region', waterArea);