Strip AES padding during fread/fwrite

I'm using libgcrypt to encrypt and decrypt files. When I take in the proper amount of bytes using fread, I need to pad it with 16-n bytes in order for it to properly be encrypted by gcry_cipher_encrypt. Upon decryption however, the null bytes/padding is still present. Is there any way to read and write in 16 byte blocks and still strip the padding at the end?

#include <stdio.h>
#include <gcrypt.h>

#define algo GCRY_CIPHER_AES128
#define mode GCRY_CIPHER_MODE_CBC
#define KEY_LENGTH 16
#define BLOCK_LENGTH 16

int main(){

    char IV[16];
    char *encBuffer = NULL;
    FILE *in, *out, *reopen;
    char *key = "A key goes here!";
    gcry_cipher_hd_t handle;
    int bufSize = 16, bytes;

    memset(IV, 0, 16);

    encBuffer = malloc(bufSize);

    in = fopen("in.txt", "r");
    out = fopen("out.txt", "w");

    gcry_cipher_open(&handle, algo, mode, 0);
    gcry_cipher_setkey(handle, key, KEY_LENGTH);
    gcry_cipher_setiv(handle, IV, BLOCK_LENGTH);

    while(1){
        bytes = fread(encBuffer, 1, bufSize, in);
        if (!bytes) break;
        while(bytes < bufSize)
            encBuffer[bytes++] = 0x0;
        gcry_cipher_encrypt(handle, encBuffer, bufSize, NULL, 0);
        bytes = fwrite(encBuffer, 1, bufSize, out);
    }

    gcry_cipher_close(handle);
    fclose(in);
    fclose(out);

    gcry_cipher_open(&handle, algo, mode, 0);
    gcry_cipher_setkey(handle, key, KEY_LENGTH);
    gcry_cipher_setiv(handle, IV, BLOCK_LENGTH);

    reopen = fopen("out.txt", "r");
    out = fopen("decoded.txt", "w");

    while(1){
        bytes = fread(encBuffer, 1, bufSize, reopen);
        if (!bytes) break;
        gcry_cipher_decrypt(handle, encBuffer, bufSize, NULL, 0);
        bytes = fwrite(encBuffer, 1, bufSize, out);
    }

    gcry_cipher_close(handle);

    free(encBuffer);

    return 0;
}

I was able to fix it by correctly storing the amount of padding and then checking for it later, suggested by zaph. I used PKCS#7 in order to determine how many bytes to write and of what type. I could've written NULL bytes, but there would've been no difference, so might as well stick to a standard.

#include <stdio.h>
#include <gcrypt.h>

#define algo GCRY_CIPHER_AES128
#define mode GCRY_CIPHER_MODE_CBC
#define KEY_LENGTH 16
#define BLOCK_LENGTH 16

int main(){

    char IV[16], *encBuffer = NULL;
    char *key = "A key goes here!";
    int bufSize = 16, bytes, i=0, padding;

    FILE *in, *out, *reopen;
    gcry_cipher_hd_t handle;

    memset(IV, 0, 16);
    encBuffer = malloc(bufSize);

    // Open in/out for reading and writing
    in = fopen("in.txt", "r");
    out = fopen("out.txt", "w");

    // Set handle for encryption
    gcry_cipher_open(&handle, algo, mode, 0);
    gcry_cipher_setkey(handle, key, KEY_LENGTH);
    gcry_cipher_setiv(handle, IV, BLOCK_LENGTH);

    // Read from in, write encrypted to out
    while(1){
        bytes = fread(encBuffer, 1, bufSize, in);
        if (!bytes) break;

        // If fread grabbed less than 16 bytes, that's our final line
        // Use the byte number for padding and pad N bytes of N
        if ( bytes < BLOCK_LENGTH ){ padding = 16-bytes; }

        while(bytes < bufSize)
            encBuffer[bytes++] = padding;
        gcry_cipher_encrypt(handle, encBuffer, bytes, NULL, 0);
        bytes = fwrite(encBuffer, 1, bufSize, out);
    }

    // Close handle and i/o files
    gcry_cipher_close(handle);
    fclose(in);
    fclose(out);

    // Set handle for decryption
    gcry_cipher_open(&handle, algo, mode, 0);
    gcry_cipher_setkey(handle, key, KEY_LENGTH);
    gcry_cipher_setiv(handle, IV, BLOCK_LENGTH);

    // Reopen outfile, open decoded file
    reopen = fopen("out.txt", "r");
    out = fopen("decoded.txt", "w");

    //Loop until EOF
    while(1){
        i=0;
        bytes = fread(encBuffer, 1, bufSize, reopen);
        if (!bytes) break;
        gcry_cipher_decrypt(handle, encBuffer, bufSize, NULL, 0);
        // Read each block and check for padding
        while ( i++ < BLOCK_LENGTH ){
            // If padding is found write 16-padding bytes
            if ( encBuffer[i] == padding ){
                bytes = fwrite(encBuffer, 1, (16-padding), out);
                return 0;
            }
        }
        // If padding isn't found, write the whole buffer
        bytes = fwrite(encBuffer, 1, bufSize, out);
    }

    // Close the handle and free the buffer
    gcry_cipher_close(handle);
    free(encBuffer);

    return 0;
}