system("stty erase ^H);
system("stty -F /dev/ttyS0 -icrnl -ixon -ixoff -opost -isig -icanon -echo");    // enter into non-canonical (raw) mode

This would be insufficient code (and poor coding practice per POSIX conventions) to put the serial port into raw or non-canonical mode.
The easiest method in C and Linux is to use the function cfmakeraw() which is available in both the GNU libc and uClibc libraries. Use the man page to obtain the details on the termios structure members that are modified by cfmakeraw().
Beware that cfmakeraw() will setup the serial port in raw mode for a data length of 8 bits and no parity, for a total character frame of 10 bits (assuming one stop bit).

The preferred method is preserving a copy of the termios stucture (for restoration on program exit) and only modifying the required flag bits (rather than writing the complete structure members).

REVISION

Code that works on my ARM SoC is:

#include <stdio.h>
#include <stdlib.h>
#include <sys/un.h>
#include <unistd.h>
#include <errno.h>
#include <fcntl.h>
#include <sys/types.h>
#include <sys/ioctl.h>
#include <sys/stat.h>
#include <sys/syslog.h>
#include <termios.h>

#define SERIALPORT_IS_CONSOLE

main()
{
    struct termios  tty;
    struct termios  savetty;
    speed_t     spd;
    unsigned int    sfd;
    unsigned char   buf[80];
    int     reqlen = 79;
    int     rc;
    int     rdlen;
    int     pau = 0;

#ifdef SERIALPORT_IS_CONSOLE
    sfd = STDIN_FILENO;
#else
    sfd = open("/dev/ttyS1", O_RDWR | O_NOCTTY);
#endif
    if (sfd < 0) {
        syslog(LOG_DEBUG, "failed to open: %d, %s", sfd, strerror(errno));
        exit (-1);
    }
    syslog(LOG_DEBUG, "opened sfd=%d for reading", sfd);

    rc = tcgetattr(sfd, &tty);
    if (rc < 0) {
        syslog(LOG_DEBUG, "failed to get attr: %d, %s", rc, strerror(errno));
        exit (-2);
    }
    savetty = tty;    /* preserve original settings for restoration */

    spd = B115200;
    cfsetospeed(&tty, (speed_t)spd);
    cfsetispeed(&tty, (speed_t)spd);

    cfmakeraw(&tty);

    tty.c_cc[VMIN] = 1;
    tty.c_cc[VTIME] = 10;

    tty.c_cflag &= ~CSTOPB;
    tty.c_cflag &= ~CRTSCTS;    /* no HW flow control? */
    tty.c_cflag |= CLOCAL | CREAD;
    rc = tcsetattr(sfd, TCSANOW, &tty);
    if (rc < 0) {
        syslog(LOG_DEBUG, "failed to set attr: %d, %s", rc, strerror(errno));
        exit (-3);
    }

    do {
        unsigned char   *p = buf;
    
        rdlen = read(sfd, buf, reqlen);
        if (rdlen > 0) {
            if (*p == '\r')
                pau = 1;
            syslog(LOG_DEBUG, "read: %d, 0x%x 0x%x 0x%x", \
                     rdlen, *p, *(p + 1), *(p + 2));
        } else {
            syslog(LOG_DEBUG, "failed to read: %d, %s", rdlen, strerror(errno));
        }
    } while (!pau);

    tcsetattr(sfd, TCSANOW, &savetty);
    close(sfd);
    exit (0);
}

The compiled program is loaded & executed on the target board.

From the host side of the serial comm link, the file seq.bin with the following contents is sent:

$ od -t x1 seq.bin
0000000 aa 02 fe
0000003

Then “ABC” is typed on the host (which is running the minicom terminal emulator program), followed by a carriage return.
The program terminates on the target, and the syslog is then examined:

# tail /var/log/messages                                                        
Sep xx xx:xx:42 atmel_soc user.info kernel: EXT3 FS on nvsram, internal journal 
Sep xx xx:xx:42 atmel_soc user.info kernel: EXT3-fs: mounted filesystem with or.
Sep xx xx:xx:42 atmel_soc user.info kernel: kjournald starting.  Commit intervas
Sep xx xx:xx:18 atmel_soc auth.info login[431]: root login on 'ttyS0'           
Sep xx xx:xx:04 atmel_soc user.debug syslog: opened sfd=0 for reading           
Sep xx xx:xx:14 atmel_soc user.debug syslog: read: 3, 0xaa 0x2 0xfe             
Sep xx xx:xx:50 atmel_soc user.debug syslog: read: 1, 0x41 0x2 0xfe              
Sep xx xx:xx:51 atmel_soc user.debug syslog: read: 1, 0x42 0x2 0xfe              
Sep xx xx:xx:51 atmel_soc user.debug syslog: read: 1, 0x43 0x2 0xfe              
Sep xx xx:xx:52 atmel_soc user.debug syslog: read: 1, 0xd 0x2 0xfe              
# 

The binary data has been received intact.

Note that since this is raw mode and the typed chars were entered relatively slowly, the read() returns “partial” data and the user program would be responsible for buffering/assembling the data into complete “messages”. If the messages are of fixed length, then c_cc[VMIN]member could be set to the message length. But beware of message framing issues and complications when frame sync is lost!