byte[] output = new byte[stream.Length];
output = stream.ToArray();
byte[] processingArray = new byte[16];

int index = 0;
int chunks = output / 16;
for(int i = 0; i < chunks; i++){
  for(int x = 0; x < 16; x++){
     processingArray[x] = output[x + index];
  }
  //do the processing on the array here
  index += 16;
}

byte[] block = new byte[16];
int bytesRead = stream.Read(block, 0, block.Length);

stream.Position = 0; // go to beginning of stream

byte[] buffer = new byte[16];
while(stream.Read(buffer, 0, buffer.Length) > 0)
{
    // process
}

MemoryStream ms;

byte[] buffer = ms.GetBuffer();
int offset = ms.Position;
int left = ms.Length - offset;

while(left != 0)
{
    // process buffer starting at offset.
}